Short Oligonucleotide Analysis Package

SOAP (Short Oligonucleotide Analysis Package) is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.

All programs in the SOAP package may be used free of charge and are distributed under the GPL open source software license.

The SOAP suite of tools can be used to perform the following genome assembly tasks:

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.

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. SOAPdenovo was used to assemble the genome of the giant panda. This was upgraded to SOAPdenovo2, which was optimized for large genomes and included the widely used GapCloser module.

SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq that was created for the 1000 Plant Genomes project.

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.

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.