{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:18:53Z","timestamp":1778055533923,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2528,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion\/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche\/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs\/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly.<\/jats:p>\n               <jats:p>Availability: inGAP is available at http:\/\/sites.google.com\/site\/nextgengenomics\/ingap<\/jats:p>\n               <jats:p>Contact: \u00a0scs@bx.psu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp615","type":"journal-article","created":{"date-parts":[[2009,10,31]],"date-time":"2009-10-31T00:13:10Z","timestamp":1256947990000},"page":"127-129","source":"Crossref","is-referenced-by-count":52,"title":["inGAP: an integrated next-generation genome analysis pipeline"],"prefix":"10.1093","volume":"26","author":[{"given":"Ji","family":"Qi","sequence":"first","affiliation":[{"name":"Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fangqing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Buboltz","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan C.","family":"Schuster","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,10,30]]},"reference":[{"key":"2023012507532366900_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. 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