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--- archive:bioinformatic_tools:phrap [2010/04/08 21:58]
svasili created
+++ archive:bioinformatic_tools:phrap [2015/07/28 06:24]
ceisenhart ↷ Page moved from bioinformatic_tools:phrap to archive:bioinformatic_tools:phrap
@@ Line 8: / Line 8: @@
   * "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]]
+PHRAP documentation available [[http://www.phrap.org/phredphrap/phrap.html | here]].
+Requires Consed or phrapview editors.
+===== Academic User Agreement =====
+Please have a look at [[http://www.phrap.org/consed/academic_agreement.txt|academic user agreement]].
+===== 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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