Banana Slug Genomics

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===== ARACHNE =====
====High Level Overview====
Arachne was the first program developed by the Broad institute to assemble "long reads from sanger-method sequencing"[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. They have a more current program named [[bioinformatic_tools:allpaths|AllPaths]] that they claim is better suited to shorter sequence reads (100+ bp)[(cite:broad)]. Arachne may be download from [[ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/|here]], and there is a [[http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page|documentation wiki]] set up for it as well.


Arachne also requires GCC-4.3+. 

====Installation====
Installed statically on isla.cse.ucsc.edu and transferred over.

Installed with boost_1.38 and gcc version 4.4.

The installed the binaries here:

/projects/lowelab/users/jstjohn/Arachne
and then I ziped them and transfered them via scp over to campusrocks.

To compile static I ran configure with “CXXFLAGS=-static”.

They also installed graphviz on the computer which is necessary to view some of the output, although I am pretty sure this isn't a pre-requisite to compile the program as the configure script never bugged me about specifying the graphviz source and/or binary.

===== References =====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~

Banana Slug Genomics

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