Record added by Jurg Ott (the original Rockefeller list)
Short Oligonucleotide Analysis Package
SOAP provides full solution to next generation sequencing data analysis. Currently, it consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder (SOAPindel), a structural variation scanner (SOAPsv) and a de novo short reads assembler (SOAPdenovo).
http://soap.genomics.org.cn/SOAPsv.html (SOAP structural variants)
Li, et al. (2008), “SOAP: short oligonucleotide alignment program”, Bioinformatics, 24:713-714.
Li, Li, Fang, et al. (2009), “SNP detection for massively parallel whole-genome resequencing”, Genome Research, 19:1124-1132.
Li, Yu, Li, Lam, Yiu, Kristiansen, Wang (2009), “SOAP2: an improved ultrafast tool for short read alignment”, Bioinformatics, 25(15):1966-1967.