SOAP (Short Oligonucleotide Analysis Package) is a suite of bioinformatics software tools enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read data.
Contents
- Functionality
- Sequence Alignment
- Genome Assembly
- Indel Discovery
- SNP Discovery
- Structural Variation Discovery
- SOAP v1
- SOAP v2
- SOAP v3
- References
All programs in the SOAP package may be used free of charge and are distributed under the GPL.
Functionality
The SOAP package can be used to perform the following tasks:
Sequence Alignment
SOAPaligner is specifically designed for fast alignment of short reads and performs favorably with respect to similar alignment tools such as Bowtie and MAQ.
Genome Assembly
SOAPdenovo is a short read denovo assembler. It is optimized for short reads such as that generated by Illumina and is capable of assembling large genomes such as the human genome. SOAPdenovo was used to assemble the genome of the giant panda.
Indel Discovery
SOAPindel is a tool to find insertions and deletions from next generation paired-end sequencing data.
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.
SOAP v1
The first release of SOAP consisted only of the sequence alignment tool SOAPaligner.
SOAP v2
SOAP v2 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 to include the new tools: SOAPdenovo, SOAPindel, SOAPsnp, and SOAPsv.
SOAP v3
SOAP v3 extended the alignment tool by being the first short-read alignment tool to utilize GPU processors. As a result of these improvements, SOAPalign significantly outperforms competing aligners Bowtie and BWA in terms of speed.