{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T15:03:03Z","timestamp":1758812583297},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications.<\/jats:p>\n               <jats:p>Availability and implementation: IonGAP is hosted by the ITER\u2019s Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http:\/\/iongap.hpc.iter.es.<\/jats:p>\n               <jats:p>Contact: \u00a0mcolesan@ull.edu.es or cflores@ull.edu.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv283","type":"journal-article","created":{"date-parts":[[2015,5,8]],"date-time":"2015-05-08T00:12:11Z","timestamp":1431043931000},"page":"2870-2873","source":"Crossref","is-referenced-by-count":13,"title":["IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data"],"prefix":"10.1093","volume":"31","author":[{"given":"Adrian","family":"Baez-Ortega","sequence":"first","affiliation":[{"name":"1 Information Technology Department, Instituto Tecnol\u00f3gico y de Energ\u00edas Renovables (ITER), Santa Cruz de Tenerife, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian","family":"Lorenzo-Diaz","sequence":"additional","affiliation":[{"name":"2 Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud P\u00fablica de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain,"},{"name":"3 Research Unit, Hospital Universitario Nuestra Se\u00f1ora de Candelaria, Santa Cruz de Tenerife, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariano","family":"Hernandez","sequence":"additional","affiliation":[{"name":"2 Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud P\u00fablica de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos Ignacio","family":"Gonzalez-Vila","sequence":"additional","affiliation":[{"name":"1 Information Technology Department, Instituto Tecnol\u00f3gico y de Energ\u00edas Renovables (ITER), Santa Cruz de Tenerife, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jose Luis","family":"Roda-Garcia","sequence":"additional","affiliation":[{"name":"4 Departamento de Ingenier\u00eda Inform\u00e1tica y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos","family":"Colebrook","sequence":"additional","affiliation":[{"name":"4 Departamento de Ingenier\u00eda Inform\u00e1tica y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Flores","sequence":"additional","affiliation":[{"name":"2 Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud P\u00fablica de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain,"},{"name":"3 Research Unit, Hospital Universitario Nuestra Se\u00f1ora de Candelaria, Santa Cruz de Tenerife, Spain,"},{"name":"5 CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,5,6]]},"reference":[{"key":"2023020202240212800_btv283-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023020202240212800_btv283-B2","first-page":"45","article-title":"Genome sequence assembly using trace signals and additional sequence information","volume":"99","author":"Chevreux","year":"1999","journal-title":"Comput. Sci. Biol."},{"key":"2023020202240212800_btv283-B3","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1093\/bioinformatics\/btu135","article-title":"Orione, a web-based framework for NGS analysis in microbiology","volume":"30","author":"Cuccuru","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B4","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"2023020202240212800_btv283-B5","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1093\/bioinformatics\/btq484","article-title":"Circoletto: visualizing sequence similarity with Circos","volume":"26","author":"Darzentas","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B6","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1186\/1471-2164-13-258","article-title":"On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer","volume":"13","author":"Doig","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020202240212800_btv283-B7","doi-asserted-by":"crossref","first-page":"2597","DOI":"10.1128\/JB.01695-07","article-title":"The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse","volume":"190","author":"Durfee","year":"2008","journal-title":"J. Bacteriol."},{"key":"2023020202240212800_btv283-B8","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/2042-5783-3-2","article-title":"Beginner\u2019s guide to comparative bacterial genome analysis using next-generation sequence data","volume":"3","author":"Edwards","year":"2013","journal-title":"Microb. Inform Exp."},{"key":"2023020202240212800_btv283-B9","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/1471-2164-15-96","article-title":"Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood","volume":"15","author":"Frey","year":"2014","journal-title":"BMC Genomics"},{"key":"2023020202240212800_btv283-B10","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3624","article-title":"Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions","volume":"15","author":"Fricke","year":"2014","journal-title":"Nat. Rev. Genetics"},{"key":"2023020202240212800_btv283-B11","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R","volume":"26","author":"Guy","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B12","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/ng.1028","article-title":"De\u00a0novo assembly and genotyping of variants using colored de Bruijn graphs","volume":"44","author":"Iqbal","year":"2012","journal-title":"Nat. Genet."},{"key":"2023020202240212800_btv283-B13","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1093\/bioinformatics\/bts673","article-title":"High-throughput microbial population genomics using the Cortex variation assembler","volume":"29","author":"Iqbal","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B14","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"2023020202240212800_btv283-B15","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/bioinformatics\/btq284","article-title":"A computational genomics pipeline for prokaryotic sequencing projects","volume":"26","author":"Kislyuk","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B16","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"2023020202240212800_btv283-B17","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btp615","article-title":"inGAP: an integrated next-generation genome analysis pipeline","volume":"26","author":"Qi","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B18","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/s10482-013-9953-x","article-title":"Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes","volume":"104","author":"Reumerman","year":"2013","journal-title":"Antonie van Leeuwenhoek"},{"key":"2023020202240212800_btv283-B19","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020202240212800_btv283-B20","doi-asserted-by":"crossref","first-page":"D391","DOI":"10.1093\/nar\/gkl791","article-title":"MvirDB\u2014a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications","volume":"35","author":"Zhou","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2870\/49035356\/bioinformatics_31_17_2870.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2870\/49035356\/bioinformatics_31_17_2870.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:48:10Z","timestamp":1675309690000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/17\/2870\/183607"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,6]]},"references-count":20,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2015,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv283","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,9,1]]},"published":{"date-parts":[[2015,5,6]]}}}