Fast and accurate short read alignment with Burrows-Wheeler transform.

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 eff

SUBMITTER: Li H 

PROVIDER: S-EPMC2705234 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature