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--- archive:bioinformatic_tools:cap3_pcap [2010/04/09 01:07]
mpcusack
+++ 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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-[[http://seq.cs.iastate.edu/cap3.html|Download Page]]
+====== CAP3 PCAP ======
-[[http://helix.nih.gov/Applications/cap3.html|Instructions for running on NIH Helix]]
-The NIH pages seems to have much more information than the Iowa State page.
+===== 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:
+==== Publications ====
-  Huang, X. and Madan, A. (1999)
+**CAP3: A DNA Sequence Assembly Program**
-  CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.
+[(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/
+==== 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 ====
+[[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~~
-  Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
-  PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170.

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