Fast and accurate long-read alignment with Burrows–Wheeler transform

Abstract

Abstract Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk

Cite this paper

Related papers

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs1997
2. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice1994
3. STAR: ultrafast universal RNA-seq aligner2012
4. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability2013
5. MUSCLE: multiple sequence alignment with high accuracy and high throughput2004