sourmash
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sourmash-bio
Quickly search, compare, and analyze genomic and metagenomic data sets.
* read kprocessor tables? * download genomes a la genome grist (UPDATE: see https://github.com/ctb/get-some-ncbi-genomes) ref https://github.com/sourmash-bio/sourmash/issues/1353
`sourmash sig merge -h` prints: >Note: `merge` only creates one output file, with one signature in it, in the JSON `.sig` format. yet it uses `sourmash_args.SaveSignaturesToLocation` internally which supports the...
First off, this is definitely an odd situation where undefined behavior is, well, undefined. In brief, when assigning taxonomies using lineages with missing ranks, such as this from the podar...
Ran sourmash gather on pig gut metagenomes against gtdbtk. Assembled MAGs from the metagenomes, then reran gather against gtdbtk + newly assembled MAGs. For most of the metagenomes, total %...
as of ~November 2023 - info copied from slack and e-mails ;). editable hackmd [here](https://hackmd.io/xlJNkhSgTPaLID6_gQzITg). note: 2023-08-17 is the cutoff date for the 1M metagenomes luiz built this index from....
it looks like it does not, which is surprising to me. Specifically, on one sample (JRH_1) I see in gather output: the recovered matches hit 73.1% of the abundance-weighted query....
While working on https://github.com/sourmash-bio/branchwater/issues/24 I needed a way to extract the manifest for an existing RevIndex, and there was no way to do it...
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Quickly search, compare, and analyze genomic and metagenomic data sets.