{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T10:38:03Z","timestamp":1758191883213,"version":"3.44.0"},"reference-count":202,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal for Parasitology"],"published-print":{"date-parts":[[2020,1]]},"DOI":"10.1016\/j.ijpara.2019.10.004","type":"journal-article","created":{"date-parts":[[2019,12,16]],"date-time":"2019-12-16T10:35:26Z","timestamp":1576492526000},"page":"1-18","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Detecting sequence variants in clinically important protozoan parasites"],"prefix":"10.1016","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1911-6866","authenticated-orcid":false,"given":"Larissa","family":"Calarco","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8711-2408","authenticated-orcid":false,"given":"Joel","family":"Barratt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.ijpara.2019.10.004_b0005","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.actatropica.2012.10.013","article-title":"Sulfadoxine-pyrimethamine resistance in Plasmodium falciparum: a zoomed image at the molecular level within a geographic context","volume":"125","author":"Abdul-Ghani","year":"2013","journal-title":"Acta Trop."},{"key":"10.1016\/j.ijpara.2019.10.004_b0010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0093766","article-title":"Fast principal component analysis of large-scale genome-wide data","volume":"9","author":"Abraham","year":"2014","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ijpara.2019.10.004_b0015","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1186\/1471-2164-13-736","article-title":"A genomic scale map of genetic diversity in Trypanosoma cruzi","volume":"13","author":"Ackermann","year":"2012","journal-title":"BMC Genom"},{"key":"10.1016\/j.ijpara.2019.10.004_b0020","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/S0166-6851(01)00245-6","article-title":"The mucin-like glycoprotein super-family of Trypanosoma cruzi: structure and biological roles","volume":"114","author":"Acosta-Serrano","year":"2001","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0025","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.mcp.2009.08.002","article-title":"A second generation multiplex PCR for typing strains of Neospora caninum using six DNA targets","volume":"24","author":"Al-Qassab","year":"2010","journal-title":"Mol Cell Prob"},{"key":"10.1016\/j.ijpara.2019.10.004_b0030","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/s13071-016-1329-4","article-title":"Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome","volume":"9","author":"Alonso","year":"2016","journal-title":"Parasit Vectors"},{"key":"10.1016\/j.ijpara.2019.10.004_b0035","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1007\/s00439-012-1213-z","article-title":"A beginners guide to SNP calling from high-throughput DNA-sequencing data","volume":"131","author":"Altmann","year":"2012","journal-title":"Hum. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0040","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0035671","article-title":"Leishmaniasis worldwide and global estimates of its incidence","volume":"7","author":"Alvar","year":"2012","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ijpara.2019.10.004_b0045","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1007\/s12088-016-0606-4","article-title":"High Throughput Sequencing: An Overview of Sequencing Chemistry","volume":"56","author":"Ambardar","year":"2016","journal-title":"Indian J Microbiol"},{"key":"10.1016\/j.ijpara.2019.10.004_b0050","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1093\/oxfordjournals.molbev.a026247","article-title":"Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum","volume":"17","author":"Anderson","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0055","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/nature12876","article-title":"A molecular marker of artemisinin-resistant Plasmodium falciparum malaria","volume":"505","author":"Ariey","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0060","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1186\/1471-2164-8-391","article-title":"Database of Trypanosoma cruzi repeated genes: 20,000 additional gene variants","volume":"8","author":"Arner","year":"2007","journal-title":"BMC Genom"},{"key":"10.1016\/j.ijpara.2019.10.004_b0065","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1056\/NEJMoa1314981","article-title":"Spread of artemisinin resistance in Plasmodium falciparum malaria","volume":"371","author":"Ashley","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ijpara.2019.10.004_b0070","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/nbt.3103","article-title":"MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island","volume":"33","author":"Ashton","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0075","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1093\/infdis\/jiy223","article-title":"Drug-resistance and population structure of Plasmodium falciparum across the Democratic Republic of Congo using high-throughput molecular inversion probes","volume":"218","author":"Aydemir","year":"2018","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ijpara.2019.10.004_b0080","first-page":"67","article-title":"Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing","volume":"13","author":"Bao","year":"2014","journal-title":"Cancer Inform."},{"key":"10.1016\/j.ijpara.2019.10.004_b0085","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1001223","article-title":"H2A.Z demarcates intergenic regions of the Plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3","volume":"6","author":"Bartfai","year":"2010","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.ijpara.2019.10.004_b0090","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.vetpar.2008.10.085","article-title":"Molecular comparison of Neospora caninum oocyst isolates from naturally infected dogs with cell culture-derived tachyzoites of the same isolates using nested polymerase chain reaction to amplify microsatellite markers","volume":"160","author":"Basso","year":"2009","journal-title":"Vet. Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0095","series-title":"Draft Genome Sequences of Leishmania (Leishmania) amazonensis, Leishmania (Leishmania) mexicana, and Leishmania (Leishmania) aethiopica, Potential etiological agents of diffuse cutaneous leishmaniasis","first-page":"8","author":"Batra","year":"2019"},{"key":"10.1016\/j.ijpara.2019.10.004_b0100","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s12862-016-0625-0","article-title":"Profiles of low complexity regions in Apicomplexa","volume":"16","author":"Battistuzzi","year":"2016","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0105","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/s12936-016-1258-x","article-title":"Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes","volume":"15","author":"Beghain","year":"2016","journal-title":"Malar. J."},{"key":"10.1016\/j.ijpara.2019.10.004_b0110","first-page":"1358","article-title":"Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success","volume":"60","author":"Bell","year":"2006","journal-title":"Evolution"},{"key":"10.1016\/j.ijpara.2019.10.004_b0115","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.ijpara.2017.09.008","article-title":"A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line","volume":"48","author":"Benavente","year":"2018","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0120","article-title":"Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi","volume":"4","author":"Berna","year":"2018","journal-title":"Microb. Genom"},{"key":"10.1016\/j.ijpara.2019.10.004_b0125","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1126\/science.1112642","article-title":"The genome of the African trypanosome Trypanosoma brucei","volume":"309","author":"Berriman","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0130","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1093\/molbev\/mss090","article-title":"Detecting selective sweeps from pooled next-generation sequencing samples","volume":"29","author":"Boitard","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0135","doi-asserted-by":"crossref","first-page":"10514","DOI":"10.1073\/pnas.0510319103","article-title":"Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii","volume":"103","author":"Boyle","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0140","doi-asserted-by":"crossref","first-page":"3960","DOI":"10.1073\/pnas.0230489100","article-title":"Sequence information can be obtained from single DNA molecules","volume":"100","author":"Braslavsky","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0145","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1101\/gr.070227.107","article-title":"Quality scores and SNP detection in sequencing-by-synthesis systems","volume":"18","author":"Brockman","year":"2008","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0150","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/S0169-5347(03)00018-1","article-title":"The utility of single nucleotide polymorphisms in inferences of population history","volume":"18","author":"Brumfield","year":"2003","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0155","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1186\/s12936-018-2503-2","article-title":"Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance","volume":"17","author":"Bruske","year":"2018","journal-title":"Malar. J."},{"key":"10.1016\/j.ijpara.2019.10.004_b0160","first-page":"6","article-title":"De novo genome assembly of a Plasmodium falciparum NF54 clone using single-molecule real-time sequencing","author":"Bryant","year":"2018","journal-title":"Genome Announc."},{"key":"10.1016\/j.ijpara.2019.10.004_b0165","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/nrmicro1351","article-title":"Trypanosoma cruzi surface mucins: host-dependent coat diversity","volume":"4","author":"Buscaglia","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0170","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.1093\/gbe\/evy188","article-title":"Genome wide identification of mutational hotspots in the apicomplexan parasite Neospora caninum and the implications for virulence","volume":"10","author":"Calarco","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0175","doi-asserted-by":"crossref","first-page":"14631","DOI":"10.1038\/s41598-018-32877-2","article-title":"Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity","volume":"8","author":"Callejas-Hernandez","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ijpara.2019.10.004_b0180","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"Carver","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0185","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2105-13-8","article-title":"An integrative variant analysis suite for whole exome next-generation sequencing data","volume":"13","author":"Challis","year":"2012","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ijpara.2019.10.004_b0190","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1093\/molbev\/msu397","article-title":"Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites","volume":"32","author":"Cheeseman","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0195","series-title":"High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology","first-page":"4","author":"Chien","year":"2016"},{"key":"10.1016\/j.ijpara.2019.10.004_b0200","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nmeth.4035","article-title":"Phased diploid genome assembly with single-molecule real-time sequencing","volume":"13","author":"Chin","year":"2016","journal-title":"Nat. Meth."},{"key":"10.1016\/j.ijpara.2019.10.004_b0205","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"10.1016\/j.ijpara.2019.10.004_b0210","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.molp.2015.02.002","article-title":"Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations","volume":"8","author":"Clevenger","year":"2015","journal-title":"Mol. Plant."},{"key":"10.1016\/j.ijpara.2019.10.004_b0215","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0220","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"Consortium","year":"2010","journal-title":"Nature"},{"issue":"Pt 1","key":"10.1016\/j.ijpara.2019.10.004_b0225","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S0031182000059217","article-title":"The epidemiology of multiple-clone Plasmodium falciparum infections in Gambian patients","volume":"103","author":"Conway","year":"1991","journal-title":"Parasitology"},{"issue":"Pt 1","key":"10.1016\/j.ijpara.2019.10.004_b0230","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1017\/S0031182000059229","article-title":"Population genetics of Plasmodium falciparum within a malaria hyperendemic area","volume":"103","author":"Conway","year":"1991","journal-title":"Parasitology"},{"key":"10.1016\/j.ijpara.2019.10.004_b0235","doi-asserted-by":"crossref","first-page":"4506","DOI":"10.1073\/pnas.96.8.4506","article-title":"High recombination rate in natural populations of Plasmodium falciparum","volume":"96","author":"Conway","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0240","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1111\/j.1365-2958.2006.05511.x","article-title":"Mutations in transmembrane domains 1, 4 and 9 of the Plasmodium falciparum chloroquine resistance transporter alter susceptibility to chloroquine, quinine and quinidine","volume":"63","author":"Cooper","year":"2007","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0245","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1073\/pnas.91.3.1143","article-title":"Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine","volume":"91","author":"Cowman","year":"1994","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"Suppl 4","key":"10.1016\/j.ijpara.2019.10.004_b0250","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2164-11-S4-S7","article-title":"NGSQC: cross-platform quality analysis pipeline for deep sequencing data","volume":"11","author":"Dai","year":"2010","journal-title":"BMC Genom"},{"key":"10.1016\/j.ijpara.2019.10.004_b0255","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/s12936-016-1139-3","article-title":"Genotyping of Plasmodium vivax by minisatellite marker and its application in differentiating relapse and new infection","volume":"15","author":"Das","year":"2016","journal-title":"Malar. J."},{"key":"10.1016\/j.ijpara.2019.10.004_b0260","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1093\/gbe\/evz129","article-title":"Nanopore sequencing significantly improves genome assembly of the protozoan parasite Trypanosoma cruzi","volume":"11","author":"Diaz-Viraque","year":"2019","journal-title":"Genome Biol Evol"},{"key":"10.1016\/j.ijpara.2019.10.004_b0265","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0270","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1101\/gr.123430.111","article-title":"Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance","volume":"21","author":"Downing","year":"2011","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0275","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.2460\/javma.1988.193.10.1259","article-title":"Neonatal Neospora caninum infection in dogs: isolation of the causative agent and experimental transmission","volume":"193","author":"Dubey","year":"1988","journal-title":"J. Am. Vet. Med. Assoc."},{"issue":"Suppl 7","key":"10.1016\/j.ijpara.2019.10.004_b0280","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s12859-016-1097-3","article-title":"Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches","volume":"17","author":"Ebbert","year":"2016","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ijpara.2019.10.004_b0285","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0290","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.1112631","article-title":"The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease","volume":"309","author":"El-Sayed","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0295","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/genetics\/149.1.189","article-title":"Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum","volume":"149","author":"Escalante","year":"1998","journal-title":"Genetics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0300","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucl Acids Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0305","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1093\/bioinformatics\/btq332","article-title":"Savant: genome browser for high-throughput sequencing data","volume":"26","author":"Fiume","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0310","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1186\/s40168-018-0540-2","article-title":"Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing","volume":"6","author":"Flaherty","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.ijpara.2019.10.004_b0315","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1186\/1471-2164-13-531","article-title":"Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei","volume":"13","author":"Franzen","year":"2012","journal-title":"BMC Genome"},{"key":"10.1016\/j.ijpara.2019.10.004_b0320","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/S0169-4758(00)01698-7","article-title":"Functional diversity in the trans-sialidase and mucin families in Trypanosoma cruzi","volume":"16","author":"Frasch","year":"2000","journal-title":"Parasitol. Today"},{"key":"10.1016\/j.ijpara.2019.10.004_b0325","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1093\/genetics\/133.3.693","article-title":"Statistical tests of neutrality of mutations","volume":"133","author":"Fu","year":"1993","journal-title":"Genetics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0330","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature01097","article-title":"Genome sequence of the human malaria parasite Plasmodium falciparum","volume":"419","author":"Gardner","year":"2002","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0335","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1186\/s12859-015-0654-5","article-title":"Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale","volume":"16","author":"Girgis","year":"2015","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ijpara.2019.10.004_b0340","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0060238","article-title":"Regulatory hotspots in the malaria parasite genome dictate transcriptional variation","volume":"6","author":"Gonzales","year":"2008","journal-title":"PLoS Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0345","article-title":"Complete and de novo assembly of the Leishmania braziliensis (M2904) genome","volume":"114","author":"Gonzalez-de la Fuente","year":"2018","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"10.1016\/j.ijpara.2019.10.004_b0350","doi-asserted-by":"crossref","first-page":"18050","DOI":"10.1038\/s41598-017-18374-y","article-title":"Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs","volume":"7","author":"Gonzalez-de la Fuente","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ijpara.2019.10.004_b0355","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1093\/bioinformatics\/btu300","article-title":"Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology","volume":"30","author":"Goodswen","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0360","doi-asserted-by":"crossref","first-page":"332","DOI":"10.3389\/fgene.2018.00332","article-title":"A gene-based positive selection detection approach to identify vaccine candidates using Toxoplasma gondii as a test case protozoan pathogen","volume":"9","author":"Goodswen","year":"2018","journal-title":"Front. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0365","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.1093\/bioinformatics\/btr427","article-title":"Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0370","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.01114-13","article-title":"Trypanosoma cruzi clone Dm28c draft genome sequence","volume":"2","author":"Grisard","year":"2014","journal-title":"Genome Announc."},{"key":"10.1016\/j.ijpara.2019.10.004_b0375","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/gm306","article-title":"Improving bioinformatic pipelines for exome variant calling","volume":"4","author":"Hanlee","year":"2012","journal-title":"Genome Med."},{"key":"10.1016\/j.ijpara.2019.10.004_b0380","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1126\/science.1150427","article-title":"Single-molecule DNA sequencing of a viral genome","volume":"320","author":"Harris","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0385","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1017\/S0031182005009790","article-title":"Complex dynamics and stability of resistance to antimalarial drugs","volume":"132","author":"Hastings","year":"2006","journal-title":"Parasitology"},{"issue":"Suppl 1","key":"10.1016\/j.ijpara.2019.10.004_b0390","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1111\/j.1755-0998.2010.02943.x","article-title":"Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges","volume":"11","author":"Helyar","year":"2011","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.ijpara.2019.10.004_b0395","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/0166-6851(95)00037-2","article-title":"Natural selection on Plasmodium surface proteins","volume":"71","author":"Hughes","year":"1995","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0400","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1111\/j.1420-9101.2011.02369.x","article-title":"The fitness of drug-resistant malaria parasites in a rodent model: multiplicity of infection","volume":"24","author":"Huijben","year":"2011","journal-title":"J. Evol. Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0405","first-page":"8","article-title":"Gene expression in Leishmania is regulated predominantly by gene dosage","author":"Iantorno","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.ijpara.2019.10.004_b0410","doi-asserted-by":"crossref","unstructured":"International HapMap, C., 2005. A haplotype map of the human genome. Nature 437, 1299-1320.","DOI":"10.1038\/nature04226"},{"key":"10.1016\/j.ijpara.2019.10.004_b0415","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.12688\/f1000research.7201.1","article-title":"MinION analysis and reference consortium: Phase 1 data release and analysis","volume":"4","author":"Ip","year":"2015","journal-title":"F1000Res"},{"key":"10.1016\/j.ijpara.2019.10.004_b0420","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1126\/science.1112680","article-title":"The genome of the kinetoplastid parasite, Leishmania major","volume":"309","author":"Ivens","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0425","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0007262","article-title":"Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections","volume":"13","author":"Jayaraman","year":"2019","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.ijpara.2019.10.004_b0430","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/ng1931","article-title":"Genome variation and evolution of the malaria parasite Plasmodium falciparum","volume":"39","author":"Jeffares","year":"2007","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0435","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-4939-1438-8_4","article-title":"A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome","volume":"1201","author":"Jeffares","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0440","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.biotechadv.2009.11.002","article-title":"Toward next-generation sequencing of mitochondrial genomes\u2013focus on parasitic worms of animals and biotechnological implications","volume":"28","author":"Jex","year":"2010","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.ijpara.2019.10.004_b0445","doi-asserted-by":"crossref","first-page":"S28","DOI":"10.1038\/ng1435","article-title":"Genetic variation, classification and 'race'","volume":"36","author":"Jorde","year":"2004","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0450","first-page":"1352","article-title":"K13-propeller polymorphisms in Plasmodium falciparum parasites from sub-Saharan Africa","volume":"211","author":"Kamau","year":"2015","journal-title":"J. Infect. Dis."},{"issue":"Suppl 1","key":"10.1016\/j.ijpara.2019.10.004_b0455","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1111\/j.1755-0998.2010.02959.x","article-title":"Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip","volume":"11","author":"Karlsson","year":"2011","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.ijpara.2019.10.004_b0460","first-page":"9","article-title":"Generations of sequencing technologies: from first to next generation","author":"Kchouk","year":"2017","journal-title":"Biol. Med."},{"key":"10.1016\/j.ijpara.2019.10.004_b0465","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1101\/gr.5318106","article-title":"Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii","volume":"16","author":"Khan","year":"2006","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0470","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.ijpara.2011.01.005","article-title":"Genetic analyses of atypical Toxoplasma gondii strains reveal a fourth clonal lineage in North America","volume":"41","author":"Khan","year":"2011","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0475","doi-asserted-by":"crossref","first-page":"e00228","DOI":"10.1128\/mBio.00228-11","article-title":"A monomorphic haplotype of chromosome Ia is associated with widespread success in clonal and nonclonal populations of Toxoplasma gondii","volume":"2","author":"Khan","year":"2011","journal-title":"MBio"},{"key":"10.1016\/j.ijpara.2019.10.004_b0480","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000404","article-title":"Selection at a single locus leads to widespread expansion of Toxoplasma gondii lineages that are virulent in mice","volume":"5","author":"Khan","year":"2009","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0485","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0490","first-page":"2283","article-title":"VarScan: variant detection in massively parallel sequencing of individual and pooled samples","volume":"25","author":"Koboldt","year":"2009","journal-title":"Bioinf"},{"key":"10.1016\/j.ijpara.2019.10.004_b0495","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.biotechadv.2016.03.001","article-title":"Making sense of genomes of parasitic worms: tackling bioinformatic challenges","volume":"34","author":"Korhonen","year":"2016","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.ijpara.2019.10.004_b0500","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nmeth.1311","article-title":"Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes","volume":"6","author":"Kozarewa","year":"2009","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ijpara.2019.10.004_b0505","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/inthealth\/ihv007","article-title":"Malaria genomics: tracking a diverse and evolving parasite population","volume":"7","author":"Kwiatkowski","year":"2015","journal-title":"Int. Health"},{"key":"10.1016\/j.ijpara.2019.10.004_b0510","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/bib\/bbv029","article-title":"Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction","volume":"17","author":"Laehnemann","year":"2016","journal-title":"Brief Bioinform."},{"key":"10.1016\/j.ijpara.2019.10.004_b0515","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/nbt.2134","article-title":"Detecting and annotating genetic variations using the HugeSeq pipeline","volume":"30","author":"Lam","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0520","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ijpara.2019.10.004_b0525","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0530","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bdq.2015.02.001","article-title":"Assessing the performance of the Oxford Nanopore Technologies MinION","volume":"3","author":"Laver","year":"2015","journal-title":"Biomol. Detect. Quantif."},{"key":"10.1016\/j.ijpara.2019.10.004_b0535","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1111\/j.1365-3024.2011.01340.x","article-title":"Genomics and integrated systems biology in Plasmodium falciparum: a path to malaria control and eradication","volume":"34","author":"Le Roch","year":"2012","journal-title":"Parasite Immunol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0540","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0099744","article-title":"ROP18 is a key factor responsible for virulence difference between Toxoplasma gondii and Neospora caninum","volume":"9","author":"Lei","year":"2014","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ijpara.2019.10.004_b0545","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ijpddr.2014.09.005","article-title":"Drug resistance analysis by next generation sequencing in Leishmania","volume":"5","author":"Leprohon","year":"2015","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"10.1016\/j.ijpara.2019.10.004_b0550","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0555","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0560","first-page":"2078","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinf"},{"key":"10.1016\/j.ijpara.2019.10.004_b0565","first-page":"713","article-title":"SOAP: short oligonucleotide alignment program","volume":"24","author":"Li","year":"2008","journal-title":"Bioinf"},{"key":"10.1016\/j.ijpara.2019.10.004_b0570","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","article-title":"SOAP2: an improved ultrafast tool for short read alignment","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0575","doi-asserted-by":"crossref","DOI":"10.1155\/2012\/251364","article-title":"Comparison of next-generation sequencing systems","volume":"2012","author":"Liu","year":"2012","journal-title":"J. Biomed. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0580","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1016\/S0140-6736(12)61728-0","article-title":"Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010","volume":"380","author":"Lozano","year":"2012","journal-title":"Lancet"},{"key":"10.1016\/j.ijpara.2019.10.004_b0585","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.gpb.2016.05.004","article-title":"Oxford nanopore MinION sequencing and genome assembly","volume":"14","author":"Lu","year":"2016","journal-title":"Gen. Prot. Bioinf."},{"key":"10.1016\/j.ijpara.2019.10.004_b0590","doi-asserted-by":"crossref","first-page":"16549","DOI":"10.1038\/s41598-018-34812-x","article-title":"A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence","volume":"8","author":"Lypaczewski","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ijpara.2019.10.004_b0595","doi-asserted-by":"crossref","first-page":"370","DOI":"10.3389\/fmicb.2017.00370","article-title":"Rhoptry protein 5 (ROP5) is a key virulence factor in Neospora caninum","volume":"8","author":"Ma","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0600","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1000644","article-title":"Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates","volume":"5","author":"Mackinnon","year":"2009","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.ijpara.2019.10.004_b0605","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nature11174","article-title":"Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing","volume":"487","author":"Manske","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0610","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1146\/annurev-anchem-062012-092628","article-title":"Next-generation sequencing platforms","volume":"6","author":"Mardis","year":"2013","journal-title":"Annu. Rev. Anal. Chem. (Palo Alto Calif)"},{"key":"10.1016\/j.ijpara.2019.10.004_b0615","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/gm543","article-title":"Choice of transcripts and software has a large effect on variant annotation","volume":"6","author":"McCarthy","year":"2014","journal-title":"Genome Med."},{"key":"10.1016\/j.ijpara.2019.10.004_b0620","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/351652a0","article-title":"Adaptive protein evolution at the Adh locus in Drosophila","volume":"351","author":"McDonald","year":"1991","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0625","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0630","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1111\/1755-0998.12324","article-title":"A first look at the Oxford Nanopore MinION sequencer","volume":"14","author":"Mikheyev","year":"2014","journal-title":"Mol. Ecol. Resour."},{"issue":"Suppl 6","key":"10.1016\/j.ijpara.2019.10.004_b0635","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1752-0509-7-S6-S8","article-title":"iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data","volume":"7","author":"Mimori","year":"2013","journal-title":"BMC Syst. Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0640","doi-asserted-by":"crossref","first-page":"13458","DOI":"10.1073\/pnas.1117047109","article-title":"Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity","volume":"109","author":"Minot","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0645","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1128\/AAC.03395-14","article-title":"Detection of single-nucleotide polymorphisms in Plasmodium falciparum by PCR primer extension and lateral flow immunoassay","volume":"59","author":"Moers","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ijpara.2019.10.004_b0650","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ng1924","article-title":"Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome","volume":"39","author":"Mu","year":"2007","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0655","doi-asserted-by":"crossref","first-page":"2398","DOI":"10.1038\/s41598-017-02724-x","article-title":"High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology","volume":"7","author":"Nag","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ijpara.2019.10.004_b0660","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/nrg3367","article-title":"Sequence assembly demystified","volume":"14","author":"Nagarajan","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0665","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000243","article-title":"Adaptive copy number evolution in malaria parasites","volume":"4","author":"Nair","year":"2008","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0670","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/molbev\/msl185","article-title":"Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites","volume":"24","author":"Nair","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0675","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1101\/gr.168286.113","article-title":"Single-cell genomics for dissection of complex malaria infections","volume":"24","author":"Nair","year":"2014","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0680","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1093\/bfgp\/elp014","article-title":"Identifying regulatory elements in eukaryotic genomes","volume":"8","author":"Narlikar","year":"2009","journal-title":"Brief Funct. Gen. Prot."},{"key":"10.1016\/j.ijpara.2019.10.004_b0685","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nrg2986","article-title":"Genotype and SNP calling from next-generation sequencing data","volume":"12","author":"Nielsen","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0690","first-page":"2589","article-title":"Close kinship within multiple-genotype malaria parasite infections","volume":"279","author":"Nkhoma","year":"2012","journal-title":"Proc. Biol. Sci."},{"key":"10.1016\/j.ijpara.2019.10.004_b0695","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.pt.2013.03.012","article-title":"1912\u20132012: a century of research on Plasmodium vivax in vitro culture","volume":"29","author":"Noulin","year":"2013","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0700","doi-asserted-by":"crossref","first-page":"11036","DOI":"10.1073\/pnas.0403151101","article-title":"Host-parasite interactions and the evolution of ploidy","volume":"101","author":"Nuismer","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0705","first-page":"28","article-title":"Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing","volume":"5","author":"O'Rawe","year":"2013","journal-title":"Gen. Med."},{"key":"10.1016\/j.ijpara.2019.10.004_b0710","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/btu168","article-title":"VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants","volume":"30","author":"Obenchain","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0715","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1373\/clinchem.2014.224360","article-title":"Bioinformatics for clinical next generation sequencing","volume":"61","author":"Oliver","year":"2015","journal-title":"Clin. Chem."},{"key":"10.1016\/j.ijpara.2019.10.004_b0720","doi-asserted-by":"crossref","first-page":"52","DOI":"10.12688\/wellcomeopenres.14571.1","article-title":"Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres","volume":"3","author":"Otto","year":"2018","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0725","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1093\/dnares\/dsu028","article-title":"Optimized whole-genome amplification strategy for extremely AT-biased template","volume":"21","author":"Oyola","year":"2014","journal-title":"DNA Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0730","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-13-1","article-title":"Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes","volume":"13","author":"Oyola","year":"2012","journal-title":"BMC Genom."},{"key":"10.1016\/j.ijpara.2019.10.004_b0735","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1093\/bib\/bbs086","article-title":"A survey of tools for variant analysis of next-generation genome sequencing data","volume":"15","author":"Pabinger","year":"2014","journal-title":"Brief Bioinform."},{"key":"10.1016\/j.ijpara.2019.10.004_b0740","doi-asserted-by":"crossref","first-page":"R52","DOI":"10.1186\/gb-2010-11-5-r52","article-title":"Towards a comprehensive structural variation map of an individual human genome","volume":"11","author":"Pang","year":"2010","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0745","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/S1368-7646(98)80007-1","article-title":"Drug resistance in Leishmania: similarities and differences to other organisms","volume":"1","author":"Papadopoulou","year":"1998","journal-title":"Drug Resist. Updat."},{"key":"10.1016\/j.ijpara.2019.10.004_b0750","article-title":"Comprehensive analysis to improve the validation rate for single nucleotide variants detected by next-generation sequencing","volume":"9","author":"Park","year":"2014","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ijpara.2019.10.004_b0755","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1093\/molbev\/msu136","article-title":"PopGenome: an efficient Swiss army knife for population genomic analyses in R","volume":"31","author":"Pfeifer","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0760","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1101\/gr.9.2.167","article-title":"Mining SNPs from EST databases","volume":"9","author":"Picoult-Newberg","year":"1999","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0765","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.ajhg.2013.08.008","article-title":"Reliable identification of genomic variants from RNA-seq data","volume":"93","author":"Piskol","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0770","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1093\/gbe\/evz017","article-title":"The tritryps comparative repeatome: insights on repetitive element evolution in trypanosomatid pathogens","volume":"11","author":"Pita","year":"2019","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0775","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1101\/gr.152201","article-title":"Low-complexity regions in Plasmodium falciparum proteins","volume":"11","author":"Pizzi","year":"2001","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0780","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1101\/gr.101063.109","article-title":"Nucleosome landscape and control of transcription in the human malaria parasite","volume":"20","author":"Ponts","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0785","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0790","doi-asserted-by":"crossref","first-page":"4052","DOI":"10.1038\/ncomms5052","article-title":"A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains","volume":"5","author":"Preston","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ijpara.2019.10.004_b0795","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1186\/1471-2164-13-341","article-title":"A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers","volume":"13","author":"Quail","year":"2012","journal-title":"BMC Genom."},{"key":"10.1016\/j.ijpara.2019.10.004_b0800","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/S0140-6736(10)60061-X","article-title":"Chagas disease","volume":"375","author":"Rassi","year":"2010","journal-title":"Lancet"},{"key":"10.1016\/j.ijpara.2019.10.004_b0805","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1038\/35002615","article-title":"Pgh1 modulates sensitivity and resistance to multiple antimalarials in Plasmodium falciparum","volume":"403","author":"Reed","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0810","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/ng1133","article-title":"Quality and completeness of SNP databases","volume":"33","author":"Reich","year":"2003","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0815","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.2741\/3840","article-title":"Lights and shadows on gene organization and regulation of gene expression in Leishmania","volume":"16","author":"Requena","year":"2011","journal-title":"Front. Biosci. (Landmark Ed.)"},{"key":"10.1016\/j.ijpara.2019.10.004_b0820","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nbt.2053","article-title":"Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing","volume":"30","author":"Reumers","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0825","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1186\/s12859-015-0801-z","article-title":"An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome","volume":"16","author":"Ribeiro","year":"2015","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ijpara.2019.10.004_b0830","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1016\/j.biotechadv.2013.01.008","article-title":"Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants","volume":"31","author":"Roeber","year":"2013","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.ijpara.2019.10.004_b0835","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1038\/nature10242","article-title":"An integrated semiconductor device enabling non-optical genome sequencing","volume":"475","author":"Rothberg","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0840","doi-asserted-by":"crossref","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP 6: DNA sequence polymorphism analysis of large data sets","volume":"34","author":"Rozas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0845","doi-asserted-by":"crossref","first-page":"8286","DOI":"10.1038\/s41598-018-26334-3","article-title":"Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum","volume":"8","author":"Runtuwene","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ijpara.2019.10.004_b0850","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature21038","article-title":"Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution","volume":"542","author":"Rutledge","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0855","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1038\/35057149","article-title":"A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms","volume":"409","author":"Sachidanandam","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.ijpara.2019.10.004_b0860","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0865","doi-asserted-by":"crossref","first-page":"4205","DOI":"10.1093\/bioinformatics\/bty518","article-title":"appreci8: a pipeline for precise variant calling integrating 8 tools","volume":"34","author":"Sandmann","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0870","doi-asserted-by":"crossref","first-page":"R227","DOI":"10.1093\/hmg\/ddq416","article-title":"A window into third-generation sequencing","volume":"19","author":"Schadt","year":"2010","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0875","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1101\/gr.101360.109","article-title":"Assembly of large genomes using second-generation sequencing","volume":"20","author":"Schatz","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0880","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.9.8.677","article-title":"dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation","volume":"9","author":"Sherry","year":"1999","journal-title":"Genome Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0885","doi-asserted-by":"crossref","first-page":"5844","DOI":"10.1073\/pnas.1203190109","article-title":"Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages","volume":"109","author":"Su","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijpara.2019.10.004_b0890","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/0092-8674(95)90055-1","article-title":"The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes","volume":"82","author":"Su","year":"1995","journal-title":"Cell"},{"key":"10.1016\/j.ijpara.2019.10.004_b0895","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism","volume":"123","author":"Tajima","year":"1989","journal-title":"Genetics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0900","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1093\/infdis\/jiu491","article-title":"Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia","volume":"211","author":"Takala-Harrison","year":"2015","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ijpara.2019.10.004_b0905","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0005463","article-title":"Parasite genomics-Time to think bigger","volume":"11","author":"Talavera-Lopez","year":"2017","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.ijpara.2019.10.004_b0910","first-page":"62","article-title":"Next-generation sequencing and bioinformatics protocol for malaria drug resistance marker surveillance","author":"Talundzic","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ijpara.2019.10.004_b0915","doi-asserted-by":"crossref","first-page":"92","DOI":"10.3389\/fbioe.2015.00092","article-title":"Detection of genomic structural variants from next-generation sequencing data","volume":"3","author":"Tattini","year":"2015","journal-title":"Front. Bioeng. Biotechnol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0920","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1126\/science.1133643","article-title":"A secreted serine-threonine kinase determines virulence in the eukaryotic pathogen Toxoplasma gondii","volume":"314","author":"Taylor","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.ijpara.2019.10.004_b0925","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt","year":"2017","journal-title":"Nucl Acids Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0930","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s00239-016-9765-5","article-title":"Finding direction in the search for selection","volume":"84","author":"Thiltgen","year":"2017","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0935","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform."},{"key":"10.1016\/j.ijpara.2019.10.004_b0940","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2019.10.004_b0945","doi-asserted-by":"crossref","first-page":"3373","DOI":"10.1093\/gbe\/evx256","article-title":"High-resolution single-cell sequencing of malaria parasites","volume":"9","author":"Trevino","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0950","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1080\/21553769.2016.1178180","article-title":"Next-generation sequencing revolution through big data analytics","volume":"9","author":"Tripathi","year":"2016","journal-title":"Front. Life Sci."},{"key":"10.1016\/j.ijpara.2019.10.004_b0955","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001868","article-title":"Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania","volume":"12","author":"Ubeda","year":"2014","journal-title":"PLoS Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b0960","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/dnares\/dsw022","article-title":"Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing","volume":"23","author":"Vembar","year":"2016","journal-title":"DNA Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0965","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1475-2875-11-41","article-title":"Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples","volume":"11","author":"Venkatesan","year":"2012","journal-title":"Malar. J."},{"key":"10.1016\/j.ijpara.2019.10.004_b0970","doi-asserted-by":"crossref","first-page":"5694","DOI":"10.3390\/ijms14035694","article-title":"Development and validation of single nucleotide polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) using high-throughput genotyping","volume":"14","author":"Vera","year":"2013","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.ijpara.2019.10.004_b0975","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/ng1930","article-title":"A genome-wide map of diversity in Plasmodium falciparum","volume":"39","author":"Volkman","year":"2007","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ijpara.2019.10.004_b0980","article-title":"Evaluation of next generation sequencing platforms for whole exome variant analysis. Clin Med","volume":"2","author":"Vyas","year":"2016","journal-title":"Biochemistry"},{"key":"10.1016\/j.ijpara.2019.10.004_b0985","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0990","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq622","article-title":"MapSplice: accurate mapping of RNA-seq reads for splice junction discovery","volume":"38","author":"Wang","year":"2010","journal-title":"Nucl Acids Res."},{"key":"10.1016\/j.ijpara.2019.10.004_b0995","doi-asserted-by":"crossref","first-page":"R128","DOI":"10.1186\/gb-2010-11-12-r128","article-title":"Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly","volume":"11","author":"Wong","year":"2010","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijpara.2019.10.004_b1000","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.csbj.2018.01.003","article-title":"A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data","volume":"16","author":"Xu","year":"2018","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.ijpara.2019.10.004_b1005","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"10.1016\/j.ijpara.2019.10.004_b1010","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."}],"container-title":["International Journal for Parasitology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0020751919303005?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0020751919303005?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T14:03:40Z","timestamp":1758117820000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0020751919303005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1]]},"references-count":202,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,1]]}},"alternative-id":["S0020751919303005"],"URL":"https:\/\/doi.org\/10.1016\/j.ijpara.2019.10.004","relation":{},"ISSN":["0020-7519"],"issn-type":[{"type":"print","value":"0020-7519"}],"subject":[],"published":{"date-parts":[[2020,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Detecting sequence variants in clinically important protozoan parasites","name":"articletitle","label":"Article Title"},{"value":"International Journal for Parasitology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijpara.2019.10.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}