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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”[1]. They have a more current program named AllPaths that they claim is better suited to shorter sequence reads (100+ bp)[1]. Arachne may be download from here, and there is a 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

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archive/bioinformatic_tools/arachne.txt · Last modified: 2015/07/27 23:22 by ceisenhart