{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T08:46:48Z","timestamp":1769849208895,"version":"3.49.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.<\/jats:p>\n               <jats:p>Results: RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers\u2019 bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code and binaries are freely available for download at http:\/\/www.seqan.de\/projects\/razers. RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X and Windows.<\/jats:p>\n               <jats:p>Contact: \u00a0david.weese@fu-berlin.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts505","type":"journal-article","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T02:27:06Z","timestamp":1345861626000},"page":"2592-2599","source":"Crossref","is-referenced-by-count":133,"title":["RazerS 3: Faster, fully sensitive read mapping"],"prefix":"10.1093","volume":"28","author":[{"given":"David","family":"Weese","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin, Takustr. 9, 14195 Berlin, Germany"}]},{"given":"Manuel","family":"Holtgrewe","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin, Takustr. 9, 14195 Berlin, Germany"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin, Takustr. 9, 14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,8,24]]},"reference":[{"key":"2023012513141390600_bts505-B1","doi-asserted-by":"crossref","first-page":"e41","DOI":"10.1093\/nar\/gkr1246","article-title":"Hobbes: optimized gram-based methods for efficient read alignment","volume":"40","author":"Ahmadi","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012513141390600_bts505-B2","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/ng.437","article-title":"Personalized copy number and segmental duplication maps using next-generation sequencing","volume":"41","author":"Alkan","year":"2009","journal-title":"Nat. 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