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algbio / practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.
BSD 2-Clause "Simplified" License
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Correctly assign the reads to the edges of wtdbg2 #192

Closed sebschmi closed 3 years ago

sebschmi commented 3 years ago

The graph of wtdbg2 is given by a .dot file, but it does not relate the reads to the edges. Currently we relate much less reads to edges than we apparently could, looking at the unitigs. We need to figure out how to mirror wtdbg2's choices there.

As a last resort, we could try to make wtdbg2 output these relations in the .dot file.

sebschmi commented 3 years ago

Instead of figuring out how wtdbg2 does it, we can just modify wtdbg2 to output the .ctg.lay file for any set of walks.