Sensitive and fast mapping of di-base encoded reads
نویسندگان
چکیده
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
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عنوان ژورنال:
- Bioinformatics
دوره 27 14 شماره
صفحات -
تاریخ انتشار 2011