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archive:bioinformatic_tools:cap3_pcap [2010/04/14 09:45] galt |
archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:29] galt |
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===== Overview ===== | ===== Overview ===== | ||
- | [[http://seq.cs.iastate.edu/cap3.html|Download Page]] | + | CAP3 assembles EST sequences with optional quality values.\\ |
- | [[http://helix.nih.gov/Applications/cap3.html|Instructions for running on NIH Helix]] | + | Can use quality values. |
- | The NIH pages seems to have much more information than the Iowa State page. | + | 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? | Would we want to look into running our data on NIH clusters? | ||
- | ===== Publications ===== | + | ==== Publications ==== |
**CAP3: A DNA Sequence Assembly Program** | **CAP3: A DNA Sequence Assembly Program** | ||
- | [(cite:CAP3> | + | [(cite:CAP3>Huang, X. and Madan, A. (1999)\\ |
- | Huang, X. and Madan, A. (1999)\\ | + | CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.)]\\ |
- | CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877. | + | |
- | )]\\ | + | |
**PCAP: A Whole-Genome Assembly Program** | **PCAP: A Whole-Genome Assembly Program** | ||
- | [(cite:PCAP> | + | [(cite:PCAP>Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)\\ |
- | 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/ | ||
+ | |||
==== Website ==== | ==== Website ==== | ||
- | [[http://seq.cs.iastate.edu/cap3.html]] | + | [[http://helix.nih.gov/Applications/cap3.html|Instructions for running on NIH Helix]] |
==== Source with Binaries and Documentation ==== | ==== Source with Binaries and Documentation ==== | ||
- | [[http://TODO]] | + | [[http://seq.cs.iastate.edu/]] |
===== References ===== | ===== References ===== |