Banana Slug Genomics

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====== Phrap ======
====== Overview ======

PHRAP : "Phragment Assembly Program". Assembles shotgun DNA  sequence data, developed by Phil Green [[http://www.phrap.org/phredphrapconsed.html | link to homepage]].
===== Key Features =====
  * Allows use of entire read. 
  * Combines user input data with internally computed data quality to improve accracy of sequence assembly.
  * "Quality value Q = -10 log10( Pe ); where Q and Pe are respectively the quality value and error probability of a particular base call."
 
PHRAP documentation available [[http://www.phrap.org/phredphrap/phrap.html | here]].

Requires Consed or phrapview editors.

===== Installation instructions =====
Phrap is now installed under /campusdata/BME235/programs/phrap following instructions received from Phil Green.

Steps followed for installation :
<code>
zcat distrib.tar.Z | tar xvf -
make
</code>

===== Other important instructions from Phil Green =====

<code>
  * If you have datasets with more than 64,000 reads, or that include
sequences longer than 64,000 bp, you will need the .manyreads and/or
.longreads versions of phrap and cross_match. These are created using the
command

> make manyreads

  * If you are operating a non-commercial (academic or government)
computer facility which provides access to several independent
investigators, you are required by the licensing agreement to set the
permissions on the executables and source code to allow execute but
not read access, so that the programs may not be copied.

  * The documentation is in three .doc files: general.doc, phrap.doc,
and swat.doc. Please read it!

</code>

**NOTE** - Currently, the permissions set are : user and group has r-x permissions and others have --x permissions for the executable files and source code files.
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