RazerS 3
作者： David Weese , Manuel Holtgrewe , Knut Reinert
DOI: 10.1093/BIOINFORMATICS/BTS505
关键词: Key (cryptography) 、 Throughput (business) 、 Sensitivity (control systems) 、 Filter (video) 、 Index (publishing) 、 Computer engineering 、 Source code 、 Theoretical computer science 、 Computer science
摘要: Motivation: During the past years, next-generation sequencing has become a key technology for many applications in biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is first step. Hence, it crucial have algorithms implementations that perform fast, with high sensitivity, are able deal long large absolute number of insertions deletions. Results: RazerS program adjustable sensitivity based on counting q-grams. this work, we propose successor 3, which now supports shared-memory parallelism, an additional seed-based filter much faster, banded version Myers’ bit-vector algorithm verification, memory-saving measures support SAM output format. This leads improved performance reads, particular, errors. We extensively compare 3 other popular mappers show its results often superior them terms while exhibiting practical competitive run times. addition, works without pre-computed index. Availability Implementation: Source code binaries freely available download at http://www.seqan.de/projects/razers. implemented C++ OpenMP under GPL license using SeqAn library Linux, Mac OS X Windows. Contact: david.weese@fu-berlin.de Supplementary information:Supplementary data Bioinformatics online.
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