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Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468. Epub 2013 Aug 23.

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Author information

  • 1Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria and Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.

Abstract

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.

AVAILABILITY:

NextGenMap source code and documentation are available at: http://cibiv.github.io/NextGenMap/.

CONTACT:

fritz.sedlazeck@univie.ac.at.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23975764
DOI:
10.1093/bioinformatics/btt468
[PubMed - indexed for MEDLINE]
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