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.
Keywords: GPU; SNP calling; SOAP; consensus; index; mapping.
Copyright © 2013 John Wiley & Sons, Inc.