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dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
http://khmer.readthedocs.io/
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write counting or presence table to disk in GFA format #726

Open mr-c opened 9 years ago

mr-c commented 9 years ago

A faster way to hand off output to assemblers; can include coverage information

Spec: http://lh3.github.io/2014/07/23/first-update-on-gfa/

ABySS implementation: https://github.com/bcgsc/abyss/tree/gfa

Javascript velvelt2gfa; spades2gfa; sga2gfa; soap2gfa; abyss2gfa https://github.com/lh3/gfatools

mr-c commented 9 years ago

Leverage the tagset for graph traversal; the list of kmers can be used as a starting point.

mr-c commented 9 years ago

Look at partitioning code.

Start with long random linear sequence for testing and get that working.

ctb commented 8 years ago

See new function traverse_linear_path in #1351, which is being used to create a compact DBG in https://github.com/spacegraphcats/spacegraphcats/, 'walk-dbg.py'.