{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T17:59:00Z","timestamp":1765389540236},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,11,11]],"date-time":"2015-11-11T00:00:00Z","timestamp":1447200000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100011310","name":"Rural and Environment Science and Analytical Services Division, Scottish Government","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100011310","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008890","name":"University of Dundee","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008890","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0801-z","type":"journal-article","created":{"date-parts":[[2015,11,11]],"date-time":"2015-11-11T11:58:51Z","timestamp":1447243131000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome"],"prefix":"10.1186","volume":"16","author":[{"given":"Antonio","family":"Ribeiro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agnieszka","family":"Golicz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine Anne","family":"Hackett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iain","family":"Milne","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gordon","family":"Stephen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Marshall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew J.","family":"Flavell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Micha","family":"Bayer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,11,11]]},"reference":[{"issue":"4","key":"801_CR1","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1016\/j.tree.2004.01.009","volume":"19","author":"PA Morin","year":"2004","unstructured":"Morin PA, Luikart G, Wayne, RK and the SNP workshop group. SNPs in ecology, evolution and conservation. Trends Ecol Evol. 2004; 19(4):208\u201316. doi: 10.1016\/j.tree.2004.01.009 .","journal-title":"Trends Ecol Evol"},{"issue":"2","key":"801_CR2","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.bej.2009.12.021","volume":"49","author":"PY Liao","year":"2010","unstructured":"Liao PY, Lee KH. From SNPs to functional polymorphism: The insight into biotechnology applications. Biochem Eng J. 2010; 49(2):149\u201358. doi: 10.1016\/j.bej.2009.12.021 .","journal-title":"Biochem Eng J"},{"issue":"831460","key":"801_CR3","first-page":"1","volume":"2012","author":"S Kumar","year":"2012","unstructured":"Kumar S, Banks TW, Cloutier S. SNP Discovery through Next-Generation Sequencing and Its Applications. Int J Plant Genomics. 2012; 2012(831460):1\u201315. doi: 10.1155\/2012\/831460 .","journal-title":"Int J Plant Genomics"},{"issue":"6","key":"801_CR4","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1111\/j.1467-7652.2012.00718.x","volume":"10","author":"K Lai","year":"2012","unstructured":"Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, et al. Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J. 2012; 10(6):743\u20139. doi: 10.1111\/j.1467-7652.2012.00718.x .","journal-title":"Plant Biotechnol J"},{"key":"801_CR5","doi-asserted-by":"crossref","unstructured":"Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC. Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects. Sci Rep. 2013;3. doi: 10.1038\/srep01512 .","DOI":"10.1038\/srep01512"},{"key":"801_CR6","unstructured":"Li H. Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples. arXiv:1404.0929v1. 2014. 1404.0929 http:\/\/arxiv.org\/abs\/1404.0929 ."},{"issue":"6","key":"801_CR7","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nrg2986","volume":"12","author":"R Nielsen","year":"2011","unstructured":"Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011; 12(6):443\u201351. doi: 10.1038\/nrg2986 .","journal-title":"Nat Rev Genet"},{"issue":"1","key":"801_CR8","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1745-6150-7-17","volume":"7","author":"J Dou","year":"2012","unstructured":"Dou J, Zhao X, Fu X, Jiao W, Wang N, Zhang L, et al. Reference-free snp calling: improved accuracy by preventing incorrect calls from repetitive genomic regions. Biol Direct. 2012; 7(1):17. doi: 10.1186\/1745-6150-7-17 .","journal-title":"Biol Direct"},{"issue":"5","key":"801_CR9","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18(5):821\u20139. doi: 10.1101\/gr.074492.107 .","journal-title":"Genome Res"},{"issue":"4","key":"801_CR10","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1073\/pnas.1017351108","volume":"108","author":"S Gnerre","year":"2011","unstructured":"Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Nat Acad Sci. 2011; 108(4):1513\u20131518. doi: 10.1073\/pnas.1017351108 , http:\/\/www.pnas.org\/content\/108\/4\/1513.full.pdf .","journal-title":"Proc Nat Acad Sci"},{"issue":"11","key":"801_CR11","doi-asserted-by":"publisher","first-page":"2270","DOI":"10.1101\/gr.141515.112","volume":"22","author":"FJ Ribeiro","year":"2012","unstructured":"Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, et al. Finished bacterial genomes from shotgun sequence data. Genome Res. 2012; 22(11):2270\u2013277. doi: 10.1101\/gr.141515.112 , http:\/\/genome.cshlp.org\/content\/22\/11\/2270.full.pdf+html .","journal-title":"Genome Res"},{"issue":"8","key":"801_CR12","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics (Oxford, England). 2013; 29(8):1072\u20131075. doi: 10.1093\/bioinformatics\/btt086 .","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"801_CR13","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012; 9(4):357\u20139. doi: 10.1038\/nmeth.1923 .","journal-title":"Nat Meth"},{"issue":"5","key":"801_CR14","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with burrows\u2013wheeler transform. Bioinforma. 2010; 26(5):589\u201395. doi: 10.1093\/bioinformatics\/btp698 , http:\/\/bioinformatics.oxfordjournals.org\/content\/26\/5\/589.full.pdf+html .","journal-title":"Bioinforma"},{"key":"801_CR15","unstructured":"Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing, arXiv:1207.3907. 2012. 1207.3907 http:\/\/arxiv.org\/abs\/1207.3907 ."},{"issue":"9","key":"801_CR16","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: A mapreduce framework for analyzing next-generation dna sequencing data. Genome Res. 2010; 20(9):1297\u2013303. doi: 10.1101\/gr.107524.110 , http:\/\/genome.cshlp.org\/content\/20\/9\/1297.full.pdf+html .","journal-title":"Genome Res"},{"issue":"5","key":"801_CR17","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation dna sequencing data. Nat Genet. 2011; 43(5):491\u20138.","journal-title":"Nat Genet"},{"issue":"5","key":"801_CR18","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1093\/bioinformatics\/bts001","volume":"28","author":"N You","year":"2012","unstructured":"You N, Murillo G, Su X, Zeng X, Xu J, Ning K, et al. SNP calling using genotype model selection on high-throughput sequencing data. Bioinforma. 2012; 28(5):643\u201350. doi: 10.1093\/bioinformatics\/bts001 .","journal-title":"Bioinforma"},{"issue":"16","key":"801_CR19","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment\/Map format and SAMtools,. Bioinforma. 2009; 25(16):2078\u2013079. doi: 10.1093\/bioinformatics\/btp352 .","journal-title":"Bioinforma"},{"issue":"3","key":"801_CR20","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403\u201310. doi: 10.1006\/jmbi.1990.9999 .","journal-title":"J Mol Biol"},{"key":"801_CR21","volume-title":"Introduction to GenStat for Windows","author":"R Payne","year":"2013","unstructured":"Payne R, Murray D, Harding S, Baird D, Soutar D. Introduction to GenStat for Windows, 16th ed. Hemel Hempstead: VSN International; 2013."},{"key":"801_CR22","doi-asserted-by":"crossref","unstructured":"IWGSC TIWGSC. A chromosome-based draft sequence of the hexaploid bread wheat (triticum aestivum) genome. Science. 2014;345(6194). doi: 10.1126\/science.1251788 .","DOI":"10.1126\/science.1251788"},{"issue":"7426","key":"801_CR23","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nature11543","volume":"491","author":"TIBGSC IBGSC","year":"2012","unstructured":"IBGSC TIBGSC. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012; 491(7426):711\u20136. doi: 10.1038\/nature11543 .","journal-title":"Nature"},{"issue":"7451","key":"801_CR24","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1038\/nature12211","volume":"497","author":"B Nystedt","year":"2013","unstructured":"Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, et al. The norway spruce genome sequence and conifer genome evolution. Nature. 2013; 497(7451):579\u201384. doi: 10.1038\/nature12211 .","journal-title":"Nature"},{"issue":"5","key":"801_CR25","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1111\/j.1755-0998.2011.03024.x","volume":"11","author":"TC Glenn","year":"2011","unstructured":"Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Res. 2011; 11(5):759\u201369. doi: 10.1111\/j.1755-0998.2011.03024.x .","journal-title":"Mol Ecol Res"},{"issue":"6814","key":"801_CR26","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/35048692","volume":"408","author":"The Arabidopsis Genome Initiative","year":"2000","unstructured":"The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000; 408(6814):796\u2013815. doi: 10.1038\/35048692 .","journal-title":"Nature"},{"issue":"1","key":"801_CR27","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1111\/j.1365-313X.2012.04894.x","volume":"70","author":"JP Hamilton","year":"2012","unstructured":"Hamilton JP, Robin Buell C. Advances in plant genome sequencing. Plant J. 2012; 70(1):177\u201390. doi: 10.1111\/j.1365-313X.2012.04894.x .","journal-title":"Plant J"},{"issue":"2","key":"801_CR28","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1101\/gr.079053.108","volume":"19","author":"MJ Chaisson","year":"2009","unstructured":"Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter?Genome Res. 2009; 19(2):336\u201346. doi: 10.1101\/gr.079053.108 .","journal-title":"Genome Res"},{"issue":"4","key":"801_CR29","doi-asserted-by":"publisher","first-page":"94825","DOI":"10.1371\/journal.pone.0094825","volume":"9","author":"Z Chang","year":"2014","unstructured":"Chang Z, Wang Z, Li G. The Impacts of Read Length and Transcriptome Complexity for De Novo Assembly: A Simulation Study. PLoS ONE. 2014; 9(4):94825. doi: 10.1371\/journal.pone.0094825 .","journal-title":"PLoS ONE"},{"issue":"12","key":"801_CR30","doi-asserted-by":"publisher","first-page":"8407","DOI":"10.1371\/journal.pone.0008407","volume":"4","author":"DR Zerbino","year":"2009","unstructured":"Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de Novo assembler. PLoS ONE. 2009; 4(12):8407. doi: 10.1371\/journal.pone.0008407 .","journal-title":"PLoS ONE"},{"key":"801_CR31","unstructured":"Earl D, Bradnam K, St. John J, Darling A, Lin D, Fass J, et al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Res. 2011. doi: 10.1101\/gr.126599.111 , http:\/\/genome.cshlp.org\/content\/early\/2011\/11\/02\/gr.126599.111.full.pdf+html ."},{"issue":"1","key":"801_CR32","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/2047-217X-2-10","volume":"2","author":"K Bradnam","year":"2013","unstructured":"Bradnam K, Fass J, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience. 2013; 2(1):10. doi: 10.1186\/2047-217X-2-10 .","journal-title":"GigaScience"},{"issue":"24","key":"801_CR33","doi-asserted-by":"publisher","first-page":"3169","DOI":"10.1093\/bioinformatics\/bts605","volume":"28","author":"NA Fonseca","year":"2012","unstructured":"Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinforma. 2012; 28(24):3169\u2013177. doi: 10.1093\/bioinformatics\/bts605 , http:\/\/bioinformatics.oxfordjournals.org\/content\/28\/24\/3169.full.pdf+html .","journal-title":"Bioinforma"},{"issue":"13","key":"801_CR34","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.1093\/bioinformatics\/btu146","volume":"30","author":"C Otto","year":"2014","unstructured":"Otto C, Stadler PF, Hoffmann S. Lacking alignments? the next-generation sequencing mapper segemehl revisited. Bioinforma. 2014; 30(13):1837\u201343. doi: 10.1093\/bioinformatics\/btu146 , http:\/\/bioinformatics.oxfordjournals.org\/content\/30\/13\/1837.full.pdf+html .","journal-title":"Bioinforma"},{"issue":"3","key":"801_CR35","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1093\/bioinformatics\/btp666","volume":"26","author":"I Milne","year":"2010","unstructured":"Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D. Tablet\u2013next generation sequence assembly visualization. Bioinformatics. 2010; 26(3):401\u20132. doi: 10.1093\/bioinformatics\/btp666 .","journal-title":"Bioinformatics"},{"issue":"2","key":"801_CR36","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/bib\/bbs012","volume":"14","author":"I Milne","year":"2013","unstructured":"Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, et al. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinforma. 2013; 14(2):193\u2013202. doi: 10.1093\/bib\/bbs012 .","journal-title":"Brief Bioinforma"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0801-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0801-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0801-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,16]],"date-time":"2020-05-16T03:07:49Z","timestamp":1589598469000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0801-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,11]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["801"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0801-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,11,11]]},"article-number":"382"}}