Obtaining unitig coordinates

[revinici]

Is there away to obtain the genome coordinates of the unitigs reported by cuttlefish? I haven't been able to find this information in any of the cuttlefish outputs or documentation. I couldn't find an answer in prior github issues or internet searches either. It seems like users would have to map the unitigs back to the reference genomes to get this information. Can someone confirm that there is no way to get this information from existing cuttlefish outputs?

[jamshed]

Hi @revinici,

Sorry for our delay in response. The genome coordinates for the unitigs can be extracted / post-processed from the GFA-reduced (or the other GFA formats) output, specifically from the path-tilings of the references, if you're using cuttlefish 1 (@rob-p: any thoughts?). Cuttlefish 2 output cannot be used to get the coordinates.