Table of Contents
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
