GFA output

[ekg]

Is it possible to obtain GFA output from the assemblies created by this pipeline?

[rchikhi]

I'd say yes at a certain condition: make sure you skip scaffolding. Please use the https://github.com/GATB/minia/blob/master/scripts/convertToGFA.py script on the final assembly fasta file (it should have the L:x:x elements in headers, indicating links between contigs in the FASTA file, which is equivalent info to GFA). When running that script, you'd need to give as input the final k value ran by the pipeline. I never really looked at that pipeline GFA, and would expect that the GFA would become disconnected at coverage gaps due to the pipeline using large k values.