All programs in the SOAP package may be used free of charge and are distributed under the
GPLopen source software license.
Functionality
The SOAP suite of tools can be used to perform the following genome assembly tasks:
Sequence Alignment
SOAPaligner (SOAP2) is specifically designed for fast alignment of short reads and performs favorably with respect to similar alignment tools such as
Bowtie and MAQ.[1]
Genome Assembly
SOAPdenovo is a short read de novo assembler utilizing
De Bruijn graph construction. It is optimized for short reads such as that generated by
Illumina and is capable of assembling large genomes such as the human genome.[2]SOAPdenovo was used to assemble the genome of the
giant panda.[3] This was upgraded to SOAPdenovo2, which was optimized for large genomes and included the widely used GapCloser module.[4]
SOAPindel is a tool to find
insertions and deletions from next generation paired-end sequencing data, providing a list of candidate
indels with quality scores.[6]
SNP Discovery
SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which enables
SNPs to be called on a newly sequenced individual.
Structural Variation Discovery
SOAPsv is a tool to find structural variations using whole genome assembly.[7]
The first release of SOAP consisted only of the
sequence alignment tool SOAPaligner.[9]
SOAP v2
SOAP v2 [1] extended and improved on SOAP v1 by significantly improving the performance of the SOAPaligner tool. Alignment time was reduced by a factor of 20-30, while memory usage was reduced by a factor of 3. Support was added for compressed file formats.
The SOAP suite was expanded then to include the new tools: SOAPdenovo 1&2, SOAPindel, SOAPsnp, and SOAPsv.
SOAP v3
SOAP v3 extended the alignment tool by being the first short-read alignment tool to utilize GPU processors.[10] As a result of these improvements, SOAPalign significantly outperformed competing aligners
Bowtie and
BWA in terms of speed.