All programs in the SOAP package may be used free of charge and are distributed under the GPL open source software license.
[4] SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq that was created for the 1000 Plant Genomes project.
[5] 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.
[7] SOAPnuke is a tool for integrated quality control and preprocessing of datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments.
[10] As a result of these improvements, SOAPalign significantly outperformed competing aligners Bowtie and BWA in terms of speed.