Looking at Assemblies
After you have run Arachne and created a draft assembly, you will want to look at your assembly. It will take a detailed understanding of your assembly before you can go about improving it. Hence Arachne provides several tools for assembly analysis. The following modules generally require a SUBDIR command-line argument, specifying the assembly location. Also note that the RUN directory, in the context of these modules, should include /work.
Text output modules
Arachne stores its data in a binary format, so you cannot examine your assembly just by looking at the first output files. However, Arachne provides text output modules, which, as the name suggests, read the binary output and produce human-readable text files.
The module VerifyAssemblyIntegrity provides a "sanity check" to make sure nothing is horribly wrong with your assembly.
The module GenerateTilings writes out an entire contig, base by base, and lines it up against the input reads that contributed to it. It writes its output in the Tilings subdirectory of SUBDIR. (GenerateTilings may take a long time to run!) A similar module is CreateAceFile, which produces ace files that can be read by Consed and look very much like the output of GenerateTilings.