FASTG or GFA input/output

dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

http://khmer.readthedocs.io/

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FASTG or GFA input/output #1467

Open ctb opened 7 years ago

ctb commented 7 years ago

After #1371 (compact De Bruijn graph work) and #1372 etc. (assembly), can we now input/output FASTG or GFA? See Twitter conversation here.

Also, what about abyss internal format - worth looking into?

ctb commented 7 years ago

Ref #726.

sjackman commented 7 years ago

:+1: for GFA

The ABySS Graphviz format is documented at https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#dot I like it because it's compatible with the family of Graphviz tools including visualization with dot, and transformation with gvpr, which is like awk for graphs. I'm happy to answer any questions about it.