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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~~
