User Tools

Site Tools


archive:bioinformatic_tools:cap3_pcap

CAP3 PCAP

Overview

CAP3 assembles EST sequences with optional quality values.
Can use quality values.

PCAP assembes large genomes.
Can use quality values and read pairs.

Developed at Iowa State University.

The NIH pages seems to have much more information than the Iowa State page.
Would we want to look into running our data on NIH clusters?

Publications

CAP3: A DNA Sequence Assembly Program[1]
PCAP: A Whole-Genome Assembly Program[2]

INSTALLING CAP3

cd /campusdata/BME235/programs
wget http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar
tar xf cap3.linux.opteron64.tar
mv CAP3 cap3
mv cap3.linux.opteron64.tar cap3/
cd cap3
cp cap3 ../../bin/

INSTALLING PCAP

cd /campusdata/BME235/programs
wget http://seq.cs.iastate.edu/PCAP/pcap.rep.linux.opteron64.tar
tar xf pcap.rep.linux.opteron64.tar
mv pcap.rep.linux.opteron64 pcap
mv pcap.rep.linux.opteron64.tar pcap/
cd pcap
cp pcap ../../bin/

The pcap package has several binaries, so we'll have to read the documentation and decide what else to copy into bin/

Running PCAP

Actually, we wanted to use autopcap, and so far we have been unable to get it to work unless we run it from a sub-directory with all the pcap-related programs in ../ which mimics the structure of their example data.
This is due to the hardwired code in autopcap to access the parent directory where pcap code is saved. The parent directory is used as default.
It took little more than 2 hrs to run the assembly on POG 454 data.

Website

Source with Binaries and Documentation

References

1. a Huang, X. and Madan, A. (1999)
CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.
2. a Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170.
You could leave a comment if you were logged in.
archive/bioinformatic_tools/cap3_pcap.txt · Last modified: 2015/07/27 23:22 by ceisenhart