Using SOAPaligner for Short Reads Alignment

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.