NextGenMap: fast and accurate read mapping in highly polymorphic genomes

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 differ...

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Bibliographic Details
Published in:Bioinformatics 2013-11, Vol.29 (21), p.2790-2791
Main Authors: Sedlazeck, Fritz J, Rescheneder, Philipp, von Haeseler, Arndt
Format: Article
Language:English
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
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Summary: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/. fritz.sedlazeck@univie.ac.at. Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btt468