Li, H., & Durbin, R. (2009). Fast and accurate short read alignment 
with Burrows–Wheeler transform. bioinformatics, 25(14), 1754-1760.

Abstract
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.