Generating a genome assembly with PCAP.
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.
Huang
Xiaoqiu
X
Iowa State University, Ames, Iowa, USA.
Yang
Shiaw-Pyng
SP
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software