Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1093/bioinformatics/bts505 | BIOINFORMATICS |
Keywords | Field | DocType |
biological sciences | Source code,Computer science,Implementation,Bioinformatics,OS X,Throughput | Journal |
Volume | Issue | ISSN |
28 | 20 | 1367-4803 |
Citations | PageRank | References |
15 | 0.89 | 11 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| David Weese | 1 | 252 | 17.79 |
| Manuel Holtgrewe | 2 | 79 | 4.05 |
| Knut Reinert | 3 | 1020 | 105.87 |