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archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:04] galt |
archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:29] galt |
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===== Overview ===== | ===== Overview ===== | ||
+ | CAP3 assembles EST sequences with optional quality values.\\ | ||
+ | Can use quality values. | ||
+ | PCAP assembes large genomes.\\ | ||
+ | Can use quality values and read pairs. | ||
- | The NIH pages seems to have much more information than the Iowa State page. | + | 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? | Would we want to look into running our data on NIH clusters? | ||
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[(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/ | ||
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==== Source with Binaries and Documentation ==== | ==== Source with Binaries and Documentation ==== | ||
- | [[http://seq.cs.iastate.edu/cap3.html]] | + | [[http://seq.cs.iastate.edu/]] |
- | [[http://seq.cs.iastate.edu/pcap.html]] | + | |
===== References ===== | ===== References ===== |