What it does

SOAP2 (SOAPaligner) is a member of the Short Oligonucleotide Analysis Package (SOAP). This is the second version of the SOAP tool which provides functionality for the accurate alignment for short reads generated by the Illumina/Solexa Genome Analyzer.

Compared to version 1 of SOAP, SOAP2 is an order of magnitude faster so that, for example, it requires only 2 minutes to align one million single-end reads onto the human reference genome. Another improvement of SOAP2 is that it now supports a wide range of read lengths.

SOAP2 has made improvements in time and space efficiency by re-implementing the basic data structures and algorithms used in SOAP1. The core algorithms and the indexing data structures (2way-BWT) were developed by T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu of the Algorithms Research group at the Department of Computer Science, The University of Hong Kong.

Using SOAP2

Short reads are mapped onto a reference genome. Index files for the reference genome are required by SOAP2 to search reads against. For testing this Galaxy wrapping of SOAP2, we have provided indices for chromosome 10 (hs_10), 12 (hs_chr22) and 22 (hu18_chr12) of the human genome.

More information

For test data and more detailed information, click here.