sourmash
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sourmash-bio
Quickly search, compare, and analyze genomic and metagenomic data sets.
back when, sourmash was a cute 'lil package that had like 5 commands: compute, search, gather, compare, plot. Now it's a tentacular monstrosity with over a dozen commands in `sig`,...
the following links are useful for tracking how many people are downloading sourmash; it's even broken out by version and architecture in some places. https://pepy.tech/project/sourmash https://anaconda.org/conda-forge/sourmash-minimal https://anaconda.org/bioconda/sourmash
at STAMPS 2022, I described the fraction of genome k-mers found (`p_match` in gather text output, `f_match_query` in the prefetch and gather CSV output) as the genomic "extent". I learned...
When running the lemonade tutorial in https://github.com/sourmash-bio/sourmash/pull/2158, the value of the `query_ani_at_rank` output by column is always empty for e.g. the `csv_summary` output format. Is this intentional and expected? If...
I've been digging into some `Storage` stuff, and thinking about: * `SourmashSignature` and how we treat signatures and `MinHash` objects as 1:1 * how selectors on databases are really tightly...
https://twitter.com/yoann_dufresne/status/1553995291589746688
For sourmash v5, we should consider changing the default output format to `-F human` for human readable output from `tax genome` and `tax metagenome`.
dumping this so it's findable  https://gist.github.com/taylorreiter/50c55359393bf2bd91a07953d6e2f9c8
@bluegenes and I have been talking about how slow protein gather is when used with genomes x gtdb. So I did some benchmarking, albeit with a metagenome. Read on! ##...
Posted here! https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/
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Quickly search, compare, and analyze genomic and metagenomic data sets.