sourmash
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sourmash-bio
Quickly search, compare, and analyze genomic and metagenomic data sets.
The root question that led to discovering https://github.com/sourmash-bio/sourmash/issues/2318 was that @bluegenes was getting unexpectedly inaccurate results from a zymo mock community analysis, and she wanted to understand why. In brief,...
when @bluegenes was digging into some classification results, she discovered that `gather` was not outputting all of the prefetch results (as evaluated by comparing to `sourmash prefetch -o ...`). (IMO...
from microbial bioinfo slack - >I downloaded the 661K_sourmash_index_scaled.sbt.zip from http://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/ and when running the search it says: ERROR: cannot use '661K_sourmash_index_scaled.sbt.zip' for this query. cannot search this SBT for...
Hi @taylorreiter, I recently tried out your tutorial to run Sourmash Gather and import the output into a phyloseq object (discovered during STAMPS!). It worked out super well on the...
in https://github.com/sourmash-bio/sra_search/pull/12, @luizirber defines some functions that seem to me like they would be nice to have in sourmash core - * `fn check_compatible_downsample` - check if two `KerMinHash` are...
https://github.com/dosisod/refurb Luiz says: >Seems like a good pairing for https://github.com/asottile/pyupgrade could also take this as an opportunity to run flake8 across the codebase.
a lot of our ancillary documentation and workflows (genome-grist and spacegraphcats) suggests doing k-mer trimming of metagenomes, e.g. with trim-low-abund. but, for gather in particular, this is not particularly important....
In https://github.com/sourmash-bio/sourmash/pull/2249, we adjusted the gather output and the `kreport` format to provide abundance-weighted results. If you run a gather _without_ abundance, ``` % sourmash gather test1.sig ../../../gtdb-rs207.genomic.k31.zip --picklist test1.gather.csv::gather...
'twould be nice to have the threshold at which matches were generated output from `sourmash gather`. https://github.com/sourmash-bio/sourmash/issues/1818 also involves adjusting sourmash gather output, so we could do both at one...
You can reach many of the sourmash developers over at [the new sourmash-bio community gitter channel](https://gitter.im/sourmash-bio/community) - hope to see you there! You can come ask for help using sourmash,...
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Quickly search, compare, and analyze genomic and metagenomic data sets.