sourmash
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sourmash-bio
Quickly search, compare, and analyze genomic and metagenomic data sets.
Punted from https://github.com/sourmash-bio/sourmash/pull/3193 - > Right now we are calculating the intersection twice, once in `disk_revindex.rs` and once in `calculate_gather_stats` in `revindex/mod.rs`. This is unnecessary, of course. But the function...
Hi, I was wondering if the gtdb reps 220 had been sketched (or is about to be)? Otherwise, would it be possible to provide/point to the command you use to...
as plugins proliferate (good? bad? who knows!) there seems to be a need for providing better docs and functions for plugins to make use of sourmash library code. areas where...
https://github.com/sourmash-bio/sourmash_plugin_directsketch
ref https://github.com/sourmash-bio/sourmash/pull/3161, "create issue around changing API documentation prior to 5.0"
in particular, https://github.com/sourmash-bio/sourmash/blob/dc9f6ea9461c45aa599b086e47f317bb26de89c6/src/sourmash/sig/__main__.py#L845 loads ALL the sketches in file into memory at once, I think because of the sketch selection in the next few lines. This should be much easier...
As I wrote in #3180, the reference genomes in gather (and prefetch) are flattened before use. This is not documented anywhere, as it turns out 😭 . Fixme please! text:...
https://github.com/mr-eyes/sourmash_plugin_dehash >In certain situations, we must reverse-hash sourmash signatures to retrieve the ACGT k-mers for further investigation or downstream analysis. This plugin performs this task efficiently but may benefit from...
https://github.com/sourmash-bio/sourmash_plugin_betterplot/ >betterplot is a sourmash plugin that provides improved plotting/viz and cluster examination for sourmash-based sketch comparisons.
https://github.com/dib-lab/sourmash_plugin_pangenomics
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Quickly search, compare, and analyze genomic and metagenomic data sets.