Using SOAPaligner for Short Reads Alignment

Shengchang Gu1, Lin Fang1, Xun Xu1

1 BGI‐Shenzhen, Shenzhen, China
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.11
DOI:  10.1002/0471250953.bi1111s44
Online Posting Date:  December, 2013
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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.

Keywords: mapping; index; consensus; SNP calling; GPU; SOAP

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Aligning a Set of Short Reads to a Reference Genome using SOAP2
  • Alternate Protocol 1: Alignment and Variation Detection Using SOAP2 and SOAPsnp
  • Alternate Protocol 2: SOAP3‐dp for Short Reads Alignment
  • Support Protocol 1: Obtaining and Installing the SOAPaligner Package
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

  Burrows, M. and Wheeler, D.J. 1994. A block‐sorting lossless data compression algorithm. Technical Report 124. Digital Equipment Corporation, Maynard, Mass.
  Hu, X., Yuan, J., Shi, Y., Lu, J., Liu, B., Li, Z., Chen, Y., Mu, D., Zhang, H., and Li, N. 2012. pIRS: Profile‐based Illumina pair‐end reads simulator. Bioinformatics 28:1533‐1535.
  Jia, W., Qiu, K., He, M., Song, P., Zhou, Q., Zhou, F., Yu, Y., Zhu, D., Nickerson, M.L., and Wan, S. 2013. SOAPfuse: An algorithm for identifying fusion transcripts from paired‐end RNA‐Seq data. Genome Biol. 14:R12.
  Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078‐2079.
  Li, R., Li, Y., Kristiansen, K., and Wang, J. 2008. SOAP: Short oligonucleotide alignment program. Bioinformatics 24:713‐714.
  Li, R., Li, Y., Fang, X., Yang, H., Wang, J., Kristiansen, K., and Wang, J. 2009a. SNP detection for massively parallel whole‐genome resequencing. Genome Res. 19:1124‐1132.
  Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K., and Wang, J. 2009b. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 25:1966‐1967.
  Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., and Kristiansen, K. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265‐272.
  Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M.H., and Wang, J. 2013. SOAPindel: Efficient identification of indels from short paired reads. Genome Res. 23:195‐200.
  Liu, C.‐M., Wong, T., Wu, E., Luo, R., Yiu, S.‐M., Li, Y., Wang, B., Yu, C., Chu, X., and Zhao, K. 2012. SOAP3: Ultra‐fast GPU‐based parallel alignment tool for short reads. Bioinformatics 28:878‐879.
  Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., and Liu, Y. 2012. SOAPdenovo2: An empirically improved memory‐efficient short‐read de novo assembler. GigaScience 1:1‐6.
  Luo, R., Wong, T., Zhu, J., Liu, C.‐M., Zhu, X., Wu, E., Lee, L.‐K., Lin, H., Zhu, W., Cheung, D.W., Ting, H.‐F., Yiu, S.‐M., Peng, S., Yu, C., Li, Y., Li, R., and Lam, T.‐W. 2013. SOAP3‐dp: Fast, accurate and sensitive GPU‐based short read aligner. PLoS ONE 8:e65632.
Internet Resources
  http://soap.genomics.org.cn/soap1/
  SOAP.
  http://soap.genomics.org.cn/soapaligner.html
  SOAP2.
  http://www.cs.hku.hk/2bwt‐tools/soap3/
  SOAP3.
  http://soap.genomics.org.cn/soap3.html
  SOAP3‐dp.
  http://www.cs.hku.hk/2bwt‐tools/soap3‐dp/
  SOAPsnp.
  http://soap.genomics.org.cn/soapsnp.html
  pIRS.
  ftp://ftp.genomics.org.cn/pub/pIRS/
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