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archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:11] galt |
archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:29] galt |
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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. | ||
Developed at Iowa State University. | Developed at Iowa State University. | ||
- | The NIH pages seems to have much more information than the Iowa State page. | + | 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? | Would we want to look into running our data on NIH clusters? | ||
Line 21: | Line 21: | ||
[(cite:PCAP>Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)\\ | [(cite:PCAP>Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)\\ | ||
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/ | ||