{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T15:51:31Z","timestamp":1778773891108,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB\/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures.<\/jats:p>\n               <jats:p>Availability: SHRiMP2 executables and source code are freely available at: http:\/\/compbio.cs.toronto.edu\/shrimp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0shrimp@cs.toronto.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr046","type":"journal-article","created":{"date-parts":[[2011,1,29]],"date-time":"2011-01-29T02:52:41Z","timestamp":1296269561000},"page":"1011-1012","source":"Crossref","is-referenced-by-count":288,"title":["SHRiMP2: Sensitive yet Practical Short Read Mapping"],"prefix":"10.1093","volume":"27","author":[{"given":"Matei","family":"David","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"}]},{"given":"Misko","family":"Dzamba","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"}]},{"given":"Dan","family":"Lister","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"}]},{"given":"Lucian","family":"Ilie","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"}]},{"given":"Michael","family":"Brudno","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"},{"name":"1 Department of Computer Science, Princeton University, 2Department of Computer Science, University of Toronto, 3Department of Computer Science, University of Western Ontario and 4Donnelly Centre, University of Toronto"}]}],"member":"286","published-online":{"date-parts":[[2011,1,28]]},"reference":[{"key":"2023012512164550800_B1","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":"2023012512164550800_B2","doi-asserted-by":"crossref","first-page":"2969","DOI":"10.1093\/bioinformatics\/btm422","article-title":"Multiple spaced seeds for homology search","volume":"23","author":"Ilie","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512164550800_B3","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":"2023012512164550800_B4","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":"2023012512164550800_B5","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1093\/bib\/bbq015","article-title":"A survey of sequence alignment algorithms for next-generation sequencing","volume":"11","author":"Li","year":"2010","journal-title":"Brief. 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