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archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:12] galt |
archive:bioinformatic_tools:cap3_pcap [2015/07/28 06:22] (current) ceisenhart ↷ Page moved from bioinformatic_tools:cap3_pcap to archive:bioinformatic_tools:cap3_pcap |
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Can use quality values. | Can use quality values. | ||
- | PCAP assembes large genomes sequences.\\ | + | PCAP assembes large genomes.\\ |
Can use quality values and read pairs. | Can use quality values and read pairs. | ||
Line 22: | Line 22: | ||
PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170.)] | PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170.)] | ||
+ | ==== 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 ==== | ==== Website ==== |