Output contigs in GFA format?

mcveanlab / mccortex

De novo genome assembly and multisample variant calling

https://github.com/mcveanlab/mccortex/wiki

MIT License

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Output contigs in GFA format? #27

Open iqbal-lab opened 8 years ago

iqbal-lab commented 8 years ago

Any plans to output your actual contigs in GFA?

noporpoise commented 8 years ago

It might be easier to 'map' a contig onto a GFA graph, since contigs should match unitigs perfectly. It just needs a hash of first & last kmers of each unitig mapping to unitig id.

Out of curiousity, what's the use case? I could throw together a script at some point.

iqbal-lab commented 8 years ago

Use-case = that GFA represents your final assembly graph. You take your links+DBG and infer contigs, plus at the end of each contig you have edges, and the string graph consisting of those contigs + edges is your final assembly.