Repository: Freie Universität Berlin, Math Department

RazerS 3: Faster, fully sensitive read mapping

Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599.

PDF (Main Article) - Published Version
PDF (Supplemental Material) - Supplemental Material

Official URL:


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. Availability and Implementation: Source code and binaries are freely available for download at RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X, and Windows.

Item Type:Article
Subjects:Biological Sciences
Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:1159
Deposited By: AG Alg BioInf
Deposited On:11 Sep 2012 14:33
Last Modified:03 Mar 2017 14:41

Repository Staff Only: item control page