UNIT 11.11 Using SOAPaligner for Short Reads Alignment

  1. Shengchang Gu,
  2. Lin Fang,
  3. Xun Xu

Published Online: 12 DEC 2013

DOI: 10.1002/0471250953.bi1111s44

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Gu, S., Fang, L. and Xu, X. 2013. Using SOAPaligner for Short Reads Alignment. Current Protocols in Bioinformatics. 11:11.11:11.11.1–11.11.17.

Author Information

  1. BGI-Shenzhen, Shenzhen, China

Publication History

  1. Published Online: 12 DEC 2013


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.


  • mapping;
  • index;
  • consensus;
  • SNP calling;
  • GPU;
  • SOAP