Key points are not available for this paper at this time.
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. 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' 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. 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.
Building similarity graph...
Analyzing shared references across papers
Loading...
David Weese
Research Institute for Sustainability at GFZ
Manuel Holtgrewe
Genetikum
Knut Reinert
Max Planck Institute for Molecular Genetics
Bioinformatics
Freie Universität Berlin
Building similarity graph...
Analyzing shared references across papers
Loading...
Weese et al. (Fri,) studied this question.
synapsesocial.com/papers/6a1109f8076612a7a7168d34 — DOI: https://doi.org/10.1093/bioinformatics/bts505