GFA2 gap edges

[sjackman]

Does SGTK support reading linkage information from GFA 2 gap edges?
https://github.com/GFA-spec/GFA-spec/blob/master/GFA2.md#gap

[olga24912]

Hi Shaun

Unfortunately, SGTK doesn’t support GFA2 format and doesn’t support GFA2 gap edges.

I think there is no problem to add GFA2 format partially and support gap edges. I will take a closer look next week and I will add a comment here before March 3 about the result.

Thanks for your feedback, it is really helpful.

Best,
Olga

[sjackman]

Thanks, Olga!
DistanceEst (from ABySS) and GapEst (https://github.com/ksahlin/GapEst) are two tools that take a BAM file and produce gap (or overlap) distance estimates. DistanceEst can output GFA2 gap edges. The author of GapEst recently contacted me, and I suggested this feature to him. It'd be great if these tools could all interoperate.

Somewhat related, have you seen this document on the topic of modular assembly components from Rayan Chikhi, Paul Medvedev, and myself?
https://github.com/GFA-spec/assembler-components
https://hackseq.github.io/modular-assembly-hs18/

[olga24912]

Hi Shaun

GFA2 is partially supported in https://github.com/olga24912/SGTK/releases/tag/v1.3

SGTK now support segment lines, dovetail edges and gap edges, but it does not support fragments and groups.

In case if GFA2 file doesn’t contain segments description(S-lines) file with contigs must be provided.

Best,
Olga

[sjackman]

That's fantastic! Thanks, Olga. I look forward to trying it out.