C. Titus Brown
C. Titus Brown
perhaps collect them from the failed processes, or something; and then report them at end.
per https://github.com/sourmash-bio/sourmash/issues/1697, >I have a set of raw reads for which I want to know if they match to a genome or not, and filter them on that basis. Usually,...
re #15 - I'm still mixed on automatically cleaning out the host DNA (since that's resource intensive and doesn't really matter to genome-grist), but per #15 it should be an...
ref https://github.com/dib-lab/genome-grist/pull/176 would be nice to have a bunch of "optional" exploration notebooks that are not run as part of the workflow, but give you entree into the various results...
an unexplored aspect of sourmash picklists is that we can run a fast search at a high scaled value (e.g. scaled=100000 is always really fast!) and then use that to...
when looking at the `subtract_gather` script for https://github.com/dib-lab/genome-grist/issues/177, I realized that we save the overlapping/multimapped reads for all genomes! it could be interesting to do something with these. not quite...
it would be nice to know how many reads were mapped to genomes, both in the multimapping and the leftover mapping parts of genome-grist. it looks like we never summarize...
This makes `genome_grist.notebooks` into an importable module and starts providing some useful classes and functions. Getting a start on https://github.com/dib-lab/genome-grist/issues/88 and https://github.com/dib-lab/genome-grist/issues/52
per https://github.com/sourmash-bio/sourmash/issues/1833#issuecomment-1033860432, it seems like we should investigate this and figure out if it works, and if so, how well.
https://github.com/dib-lab/genome-grist/pull/173 fixes a problem where 'gather' wasn't using the right ksize/moltype, but didn't add tests.