Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TLDR
Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.Abstract:
Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.
Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.
Availability: http://maq.sourceforge.net
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Citations
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Fast gapped-read alignment with Bowtie 2
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References
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MOM: maximum oligonucleotide mapping.
Hugh L. Eaves,Yuan Gao +1 more
TL;DR: This work has developed a program, Maximum Oligonucleotide Mapping (MOM), based on the concept of query matching that is designed to capture a maximal length match within the short read satisfying the user defined error parameters.
Journal ArticleDOI
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches
You Jung Kim,Nikhil Teletia,Victor Ruotti,Christopher G. Maher,Arul M. Chinnaiyan,Ron Stewart,James A. Thomson,Jignesh M. Patel +7 more
TL;DR: ProbMatch has been used to align 169,095 Illumina GAII reads against the human genome, which could not be mapped by ELAND, and found alignments for 28,625 reads of the 169,000 reads in less than 3 h.