UNIT 11.11 Using SOAPaligner for Short Reads Alignment. Issue 1 (12th December 2013)

• Record Type: Journal Article
• Authors: Gu, Shengchang; Fang, Lin; Xu, Xun
• Is Part Of: Current protocols in bioinformatics. Volume 44:Issue 1(2013)
• Page Start: 11.11.1
• Page End: 11.11.17
• Publication Date: 2013-12-12
• Subjects: mapping -- index -- consensus -- SNP calling -- GPU -- SOAP; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi1111s44
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: This unit shows how to use the SOAPaligner package to align short reads to reference. The use of the two most common versions of SOAPaligner, SOAP2 and SOAP3‐dp, will be described in detail. The unit also includes a protocol for SNP calling from SOAP2 alignment with SOAPsnp. Curr. Protoc. Bioinform . 44:11.11.1‐11.11.17. © 2013 by John Wiley & Sons, Inc.