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