Banana Slug Genomics

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====== 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/

==== 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~~
Banana Slug Genomics

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