{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T13:19:39Z","timestamp":1722691179827},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Detection of single nucleotide polymorphisms (SNPs) has been a major application in processing second generation sequencing (SGS) data. In principle, SNPs are called on single base differences between a reference genome and a sequence generated from SGS short reads of a sample genome. However, this exercise is far from trivial; several parameters related to sequencing quality, and\/or reference genome properties, play essential effect on the accuracy of called SNPs especially at shallow coverage data. In this work, we present Slider II, an alignment and SNP calling approach that demonstrates improved algorithmic approaches enabling larger number of called SNPs with lower false positive rate. In addition to the regular alignment and SNP calling, as an optional feature, Slider II is capable of utilizing information about known SNPs of a target genome, as priors, in the alignment and SNPs calling to enhance it's capability of detecting these known SNPs and novel SNPs and mutations in their vicinity.<\/jats:p>\n               <jats:p>Contact: \u00a0nmalhis@bcgsc.ca<\/jats:p>\n               <jats:p>Supplementary information and availability: \u00a0Supplementary data are available at Bioinformatics online and at http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/SliderII<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq092","type":"journal-article","created":{"date-parts":[[2010,2,28]],"date-time":"2010-02-28T01:13:01Z","timestamp":1267319581000},"page":"1029-1035","source":"Crossref","is-referenced-by-count":41,"title":["High quality SNP calling using Illumina data at shallow coverage"],"prefix":"10.1093","volume":"26","author":[{"given":"Nawar","family":"Malhis","sequence":"first","affiliation":[{"name":"Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada"}]},{"given":"Steven J. M.","family":"Jones","sequence":"additional","affiliation":[{"name":"Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada"}]}],"member":"286","published-online":{"date-parts":[[2010,2,26]]},"reference":[{"key":"2023012508075256300_B1","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":"2023012508075256300_B2","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012508075256300_B3","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508075256300_B4","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508075256300_B5","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":"2023012508075256300_B6","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1093\/bioinformatics\/btn416","article-title":"ZOOM! Zillions of oligos mapped","volume":"24","author":"Lin","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508075256300_B7","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1093\/bioinformatics\/btn565","article-title":"Slider - maximum use of probability information for alignment of short sequence reads and SNP detection","volume":"25","author":"Malhis","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508075256300_B8","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/70570","article-title":"A general approach to single-nucleotide polymorphism discovery","volume":"23","author":"Marth","year":"1999","journal-title":"Nat. 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