{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T18:54:42Z","timestamp":1722711282307},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Modern sequencing instruments have the capability to produce millions of short reads every day. The large number of reads produced in conjunction with variations between reads and reference genomic sequences caused both by legitimate differences, such as single-nucleotide polymorphisms and insertions\/deletions (indels), and by sequencer errors make alignment a difficult and computationally expensive task, and many reads cannot be aligned. Here, we introduce a new alignment tool, SRmapper, which in tests using real data can align 10s of billions of base pairs from short reads to the human genome per computer processor day. SRmapper tolerates a higher number of mismatches than current programs based on Burrows\u2013Wheeler transform and finds about the same number of alignments in 2\u20138\u00d7 less time depending on read length (with higher performance gain for longer read length). The current version of SRmapper aligns both single and pair-end reads in base space fastq format and outputs alignments in Sequence Alignment\/Map format. SRmapper uses a probabilistic approach to set a default number of mismatches allowed and determines alignment quality. SRmapper\u2019s memory footprint (\u223c2.5 GB) is small enough that it can be run on a computer with 4 GB of random access memory for a genome the size of a human. Finally, SRmapper is designed so that its function can be extended to finding small indels as well as long deletions and chromosomal translocations in future versions.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.umsl.edu\/\u223cwongch\/software.html.<\/jats:p>\n               <jats:p>Contact: \u00a0wongch@umsl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts712","type":"journal-article","created":{"date-parts":[[2012,12,25]],"date-time":"2012-12-25T03:12:57Z","timestamp":1356405177000},"page":"316-321","source":"Crossref","is-referenced-by-count":12,"title":["SRmapper: a fast and sensitive genome-hashing alignment tool"],"prefix":"10.1093","volume":"29","author":[{"given":"Paul M.","family":"Gontarz","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, St. Louis, MO 63121, USA"}]},{"given":"Jennifer","family":"Berger","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, St. Louis, MO 63121, USA"}]},{"given":"Chung F.","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, St. Louis, MO 63121, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,12,24]]},"reference":[{"key":"2023012810210728200_bts712-B1","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1093\/bioinformatics\/btr046","article-title":"SHRiMP2: sensitive yet practical short read mapping","volume":"27","author":"David","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810210728200_bts712-B2","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II","volume":"8","author":"Ewing","year":"1998","journal-title":"Error probabilities. Genome Res."},{"key":"2023012810210728200_bts712-B3","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","article-title":"Base-calling of automated sequencer traces using phred. I","volume":"8","author":"Ewing","year":"1998","journal-title":"Accuracy assessment. Genome Res."},{"key":"2023012810210728200_bts712-B4","doi-asserted-by":"crossref","first-page":"e7767","DOI":"10.1371\/journal.pone.0007767","article-title":"BFAST: an alignment tool for large scale genome resequencing","volume":"4","author":"Homer","year":"2009","journal-title":"PLoS ONE"},{"key":"2023012810210728200_bts712-B5","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":"2023012810210728200_bts712-B6","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":"2023012810210728200_bts712-B7","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":"2023012810210728200_bts712-B8","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":"2023012810210728200_bts712-B9","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":"2023012810210728200_bts712-B10","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1145\/1989323.1989370","article-title":"WHAM: A high-throughput sequence alignment method","volume-title":"Proceedings of the ACM SIGMOD International Conference on Management of Data, SIGMOD 2011","author":"Li","year":"2011"},{"key":"2023012810210728200_bts712-B11","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1101\/gr.111120.110","article-title":"Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads","volume":"21","author":"Lunter","year":"2011","journal-title":"Genome Res."},{"key":"2023012810210728200_bts712-B12","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/978-1-60327-367-1_12","article-title":"Whole genome sequencing","volume":"628","author":"Ng","year":"2010","journal-title":"Methods Mol. Biol."},{"key":"2023012810210728200_bts712-B13","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1101\/gr.194201","article-title":"SSAHA: a fast search method for large DNA databases","volume":"11","author":"Ning","year":"2001","journal-title":"Genome Res."},{"key":"2023012810210728200_bts712-B14","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1007\/s13353-011-0057-x","article-title":"Sequencing technologies and genome sequencing","volume":"52","author":"Pareek","year":"2011","journal-title":"J. Appl. Genet."},{"key":"2023012810210728200_bts712-B15","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1038\/ng.955","article-title":"Mutations in BRIP1 confer high risk of ovarian cancer","volume":"43","author":"Rafnar","year":"2011","journal-title":"Nat. Genet."},{"key":"2023012810210728200_bts712-B16","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/3\/316\/48892384\/bioinformatics_29_3_316.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/3\/316\/48892384\/bioinformatics_29_3_316.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T11:39:26Z","timestamp":1674905966000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/3\/316\/257957"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12,24]]},"references-count":16,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2013,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts712","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,2,1]]},"published":{"date-parts":[[2012,12,24]]}}}