Motivation: During the last years NGS 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 indels.
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 competetive run times. In addition, RazerS 3 works without a precomputed index.
- import of FASTA/FASTQ read and genome files
- 5 output formats (including SAM)
- reads can be of arbitrary length
- supports Hamming and edit distance read mapping with configurable error rates
- supports paired-end read mapping
- configurable and predictable sensitivity (runtime/sensitivity tradeoff)
- key improvements (compared to RazerS):
- multicore parallelization
- additional pigeonhole filter optimized for low error-rates with controllable sensitivity
- banded Myers’ algorithm for verification
- full sensitivity under the definition given in Rabema
- SAM output
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.
- Download the binaries
- View the source code and README on GitHub
- The previous version of RazerS can be found here
- Check out our newer, faster read aligner Yara
- Weese, D., Holtgrewe M., & Reinert, K. (2012). RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28(20), 2592–2599.
- Weese, D., Emde, A.-K., Rausch, T., Döring, A., & Reinert, K. (2009). RazerS – Fast read mapping with sensitivity control. Genome Research, 19(9), 1646–1654.
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