More details on w2rap-contigger step 5 needed - run with 100bp PE short reads (Illumina) about w2rap-contigger

[bjclavijo]

Hi Lan,

Sorry about the delay, we've not been keeping a very keen eye on issues lately!

Yes w2rap-contigger will run OK with 100bp reads as long as you set large K to a value smaller than 100 (which you have done).
Step 5 gets on to use all processors just after the point you get to, so I would recommend running on 16 to 32 cpus if possible. What is a bit strange in your case is that you have WAY too many unsatisfied clusters. That points to the graph on the first steps being too disconnected. I notice you're using trimmed reads, you probably want to use reads without trimming, and also have a look at your k-mer spectrum to check what you're against (use KAT for that, or any other k-mer analysis).

Best,

bj