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?

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

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/

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/

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.

Instructions for running on NIH Helix

http://seq.cs.iastate.edu/