soapaligner - 2.20-3 main

This package addresses a common problem in bioinformatics that has
become routine now also in clinical research: the assembly and
comparison of the very long genomic DNA sequences from many
short reads that the machines provide.
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SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
Package (SOAP) and an updated version of SOAP software for short
oligonucleotide alignment (soap v1). The new program features in super
fast and accurate alignment for huge amounts of short reads generated by
Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order
of magnitude faster. It require only 2 minutes aligning one million
single-end reads onto the human reference genome. Another remarkable
improvement of SOAPaligner is that it now supports a wide range of the
read length.
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SOAPaligner/soap2 benefitted in time and space efficiency by a revolution
in the basic data structures and algorithms used. The core algorithms and
the indexing data structures (2way-BWT) are developed by the algorithms
research group of the Department of Computer Science, the University
of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).