Generating a genome assembly with PCAP

Current Protocols in Bioinformatics
Xiaoqiu Huang, Shiaw-Pyng Yang

Abstract

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.

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Citations

Feb 10, 2012·PloS One·Francesco VezziBud Mishra
Apr 14, 2010·Nucleic Acids Research·Ernesto PicardiGraziano Pesole
Apr 15, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Min LiYi Pan
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Oct 28, 2019·BMC Bioinformatics·Nauman AhmedZaid Al-Ars
Nov 22, 2016·Nature Structural & Molecular Biology·Alexei V LobanovVadim N Gladyshev
Oct 28, 2008·Bioinformatics·Jason R MillerGranger Sutton

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