Open standage opened 6 years ago
Most of this would be implemented in khmer-land. See https://github.com/dib-lab/khmer/issues/1379 and https://github.com/dib-lab/khmer/pull/1392 for relevant threads in that project.
Investigating this in https://github.com/dib-lab/khmer/pull/1874.
After counting k-mers for each control sample, we should investigate composing the counttables into a single nodetable before running
kevlar novel
. This should a couple of synergistic benefits.The cost is, of course, another pass over the "data". But it should be possible to build a nodetable directly from the underlying counttables themselves without iterating over the reads again. So "data" should be quite small and manageable.