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?
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.