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.

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