sourmash

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should we add an `Index.get` method (or something similar) to retrieve signatures?

2

In https://github.com/sourmash-bio/sourmash/pull/1837, we change `sourmash sig extract` to identify signatures to extract using manifest rows, and then have to convert the manifest rows into a manifest and then from there...

ctb

FracMinHash containment to ANI conversion

4

ref ANI estimation PR #1788 I've been using our forthcoming ANI utilities to estimate pairwise ANI between GTDB genomes. From these data, we can examine the average containment --> ANI...

bluegenes

rationalize python and rust code

2

With the updated rust core, we need to go through and rationalize (and unify) rust and python code so we don't, for example, create sigs/zips that break rust assumptions. from...

bluegenes

Sourmash tax metagenome fails to properly summarize at species rank

2

Hi! Im using sourmash version 4.8.3 I have a gather.csv, with multiple hits on Listeria monocytogenes (File: ZymoLog_20231221_GBdbs.gather.csv) sourmash tax metagenome -g FILENAME.gather.csv -t /Sourmash_gb_databases/genbank-2022.03-*.lineages.csv.gz -F krona --rank species --output-base...

vehuardo

`sig describe` error when subdirectory name contains "sourmash"

1

Hi, I have found that `sourmash sig describe` returns an error if the signature file is located in a subdirectory that contains the string "sourmash". I am running sourmash version...

ezherman

document (and upgrade) windows support

8

turns out [we've supported windows](https://github.com/sourmash-bio/sourmash/issues/1004#issuecomment-635708595) for a little while, which I'd forgotten! So people have been downloading `sourmash-minimal` on conda-forge (which supports Windows builds) and then installing extra deps themselves!...

ctb

Adding more signatures to a database file

2

Hello! I got a database file with signatures, a zip file. Can I add new signatures to this, using sourmash cat? I would like to add the same signatures to...

AnneliektH

what is the right way to save output from `tax metagenome`?

1

do you use `-o` or use stdout redirect or ...? It seems to differ from output format to output format, too?

ctb

thoughts on finding all strains of a bacterial species in multiple metagenomes

1

request sent privately: >I am interested in finding strains of an bacteria (say E. Coli) in ~100 metagenomes. What’s the best way to do this? Misc thoughts: * suggest adopting...

ctb

here, we are merging all genomes under a given species or genus into a single sketch, representing that species or genus. see https://github.com/ctb/2022-database-covers/pull/4 for code sort of like the cover...

ctb