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Bioinformatics. 2011 Jul 15;27(14):1915-21. doi: 10.1093/bioinformatics/btr303. Epub 2011 May 17.

Sensitive and fast mapping of di-base encoded reads.

Author information

1
Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-5065, USA.

Erratum in

  • Bioinformatics. 2012 Jan 1;28(1):150.

Abstract

MOTIVATION:

Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of read mapping are crucial to determining the full spectrum of single nucleotide variants (SNVs) as well as structural variants (SVs) in the donor genomes analyzed.

RESULTS:

We present drFAST, a read mapper designed for di-base encoded 'color-space' sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. We show that drFAST is more sensitive in comparison to all commonly used aligners such as Bowtie, BFAST and SHRiMP. drFAST is also faster than both BFAST and SHRiMP and achieves a mapping speed comparable to Bowtie.

AVAILABILITY:

The source code for drFAST is available at http://drfast.sourceforge.net

PMID:
21586516
PMCID:
PMC3129524
DOI:
10.1093/bioinformatics/btr303
[Indexed for MEDLINE]
Free PMC Article
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