I have a new de novo assembly that I constructed with ALLPATHS-LG using three sequenced libraries (200kb, 3kb and 8kb mate-pairs). I would like to apply ATLAS-link (and ATLAS-gapfill) to this assembly, but need to resolve some issues with file preparation before I run this analysis.
One of the three required input files for ATLAS-link is a .contig file containing the assembly information that needs to be in the TIGR Assembler’s adaptation of the GDE alignment format. My current assembly output are all in FASTA format. I need to first confirm that my assembly file (final.assembly.fasta) contains the information to go into the .contig file, and then need to perform the file conversion. Any suggestions on how this can be done would be most welcome; I have found a website that will convert between the two file formats but is unable to complete the conversion (likely due to the file size). Anyone out there have a script that can do this?