NextGenMap: fast and accurate read mapping in highly polymorphic genomes

• Published in: Bioinformatics Vol. 29; no. 21; pp. 2790 - 2791
• Main Authors: Sedlazeck, Fritz J, Rescheneder, Philipp, von Haeseler, Arndt
• Format: Journal Article
• Language: English
• Published: England 01-11-2013
• Subjects: Bioinformatics; Contact; Genome; Genomes; Genomics - methods; Handles; Hardware; High-Throughput Nucleotide Sequencing - methods; Mapping; On-line systems; Polymorphism, Genetic; Sequence Alignment - methods; Sequencing; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btt468

When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology.
NextGenMap source code and documentation are available at: http://cibiv.github.io/NextGenMap/.
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Supplementary data are available at Bioinformatics online.