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archive:bioinformatic_tools:cap3_pcap

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A PCRE internal error occured. This might be caused by a faulty plugin

====== CAP3 PCAP ====== ===== Overview ===== 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? ==== Publications ==== **CAP3: A DNA Sequence Assembly Program** [(cite:CAP3>Huang, X. and Madan, A. (1999)\\ CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.)]\\ **PCAP: A Whole-Genome Assembly Program** [(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.)] ==== 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/ 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. ==== Website ==== [[http://helix.nih.gov/Applications/cap3.html|Instructions for running on NIH Helix]] ==== Source with Binaries and Documentation ==== [[http://seq.cs.iastate.edu/]] ===== References ===== <refnotes>notes-separator: none</refnotes> ~~REFNOTES cite~~

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archive/bioinformatic_tools/cap3_pcap.1276110304.txt.gz · Last modified: 2010/06/09 19:05 by svasili