UNIT 11.3 Generating a Genome Assembly with PCAP

  1. Xiaoqiu Huang1,
  2. Shiaw-Pyng Yang2

Published Online: 1 OCT 2005

DOI: 10.1002/0471250953.bi1103s11

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Huang, X. and Yang, S.-P. 2005. Generating a Genome Assembly with PCAP. Current Protocols in Bioinformatics. 11:11.3:11.3.1–11.3.23.

Author Information

  1. 1

    Iowa State University, Ames, Iowa

  2. 2

    Washington University Medical School, St. Louis, Missouri

Publication History

  1. Published Online: 1 OCT 2005
  2. Published Print: SEP 2005


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.


  • Whole-Genome Shotgun Sequencing;
  • Genome Assembly