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Fast and accurate short read alignment with Burrows-Wheeler transform (2009)
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| Venue: | BIOINFORMATICS, 2009, ADVANCE ACCESS |
| Citations: | 2090 - 24 self |
BibTeX
@MISC{Li09fastand,
author = {Heng Li and Richard Durbin},
title = {Fast and accurate short read alignment with Burrows-Wheeler transform},
year = {2009}
}
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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 hashtable 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 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 ∼10–20X faster than MAQ while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM format. Variant calling and other downstream analyses after the alignment can be achieved with the open-source SAMtools software package.
Keyphrases
burrows-wheeler transform accurate short read alignment short read color space read single-end read new dna sequencing technology similar accuracy human genome downstream analysis real data backward search ab solid machine alignment program single individual large reference sequence open-source samtools software package base space read first generation enormous amount new standard sam format new read alignment package
