ILRI Research Computing

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====== COPEread ======

COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.

===== Information =====

  * Latest Version: 1.1.2
  * Added: February, 2017
  * Link: https://sourceforge.net/projects/coperead/

===== Usage =====

See versions of COPEread which are available:
<code>$ module avail coperead/1.1.2</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ wget -qO- "https://downloads.sourceforge.net/project/coperead/src/cope-src-v1.1.2.tgz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fcoperead%2F&ts=1486559606&use_mirror=netix" | tar xzv
$ scl enable devtoolset-3 bash
$ sudo mkdir -p /export/apps/coperead/1.1.2/
$ sudo chown -R joguya:joguya /export/apps/coperead/1.1.2/
$ chmod +x src/cope/configure
$ PREFIX=/export/apps/cope/1.1.2/ make
$ PREFIX=/export/apps/cope/1.1.2/ make install 
$ sudo chown -R root:root /export/apps/coperead/1.1.2/</code>