Generating a Genome Assembly with PCAP

Xiaoqiu Huang1, Shiaw‐Pyng Yang2

1 Iowa State University, Ames, Iowa, 2 Washington University Medical School, St. Louis, Missouri
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.3
DOI:  10.1002/0471250953.bi1103s11
Online Posting Date:  October, 2005
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This unit describes how to use the Parallel Contig Assembly Program (PCAP) to assemble the data produced by a whole‐genome shotgun sequencing project. We present a basic protocol for using PCAP on a multiprocessor computer in a 300‐Mb genome assembly project. A support protocol to prepare input files for PCAP is also described. Another basic protocol for using PCAP on a distributed cluster of computers in a 3‐Gb genome assembly project is presented, in addition to suggestions for understanding results from PCAP.

Keywords: Whole‐Genome Shotgun Sequencing; Genome Assembly

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Table of Contents

  • Basic Protocol 1: Producing an Assembly with PCAP Using an Example Data Set
  • Support Protocol 1: Downloading and Installing PCAP
  • Support Protocol 2: Preparation of Input Files
  • Support Protocol 3: Generating the fofn.con File
  • Basic Protocol 2: Generating a Large‐Scale Assembly with PCAP Using Distributed Computing
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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  Havlak, P., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.‐Z., Weinstock, G.M., and Gibbs, R. 2004. The Atlas genome assembly system. Genome Res. 14:721‐732.
  Huang, X. and Madan, A. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9:868‐877.
  Huang, X., Wang, J., Aluru, S., Yang, S.‐P., and Hillier, L. 2003. PCAP: A whole‐genome assembly program. Genome Res. 13:2164‐2170.
  Jaffe, D.B., Butler, J., Gnerre, S., Mauceli, E., Lindblad‐Toh, K., Mesirov, J.P., Zody, M.C. and Lander, E.S. 2003. Whole‐genome sequence assembly for mammalian genomes: ARACHNE 2. Genome Res. 13:91‐96.
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  Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou, H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley, E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z., Liang, Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X., Rubin, G.M., Adams, M.D., and Venter, J.C. 2000. A whole‐genome assembly of Drosophila. Science 287:2196‐2204.
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Key References
   Huang et al., 2003. See above.
  This article describes the methods used in PCAP in detail.
Internet Resources
  This site contains documentation on PCAP and example test data sets.
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