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Right now, each differential hash is searched individually in `sourmash search`, but it may be better to use `sourmash gather`, as suggested by @bluegenes. If I understand correctly, what `gather` doe…
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When all samples have less than `params.lowread_filter` reads, the pipeline errors at qiime_datamerge step. The ideal behavior should be the pipeline still finishes and produces report, but with a mes…
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Hi dev team,
I suggested that the branch water web tool support searching with sourmash signatures alongside the FASTA files, and @luizirber mentioned we would need to create PR for this feature he…
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mentioned in #30
we could split classification from decontamination.
if we separated out classification from decontam, we could provide both lightweight (sourmash lca) and heavier (sourmash lca…
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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 4.8.5.
## Set…
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Hello Daniel,
I am attaching a real-world genome from the global Tara Ocean Metagenomic study, against all GTDB genomes (https://data.ace.uq.edu.au/public/gtdb/data/releases/release207/207.0/genomi…
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while I'm thinking about it... it would be nice to move towards genuinely interactive search, gather,and MAGsearch.
greyhound #1226 and greyhound.sourmash.bio/ is super cool, of course, but it's "o…
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This is related to issue #189 raised earlier.
My student Vladislav and I are using charcoal to decontaminate draft genome assemblies of nematodes. charcoal is wondrously efficient at ridding such …
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we are using GTDB taxonomy because -
* GTDB provides a nice collection of representative genomes
* GTDB provides species clusters based on ANI, which matches the approach used in charcoal
* the g…
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This is a list of repositories for sourmash, software for rapidly searching and analyzing genomes and metagenomes!
The main repository - [sourmash-bio/sourmash](https://github.com/sourmash-bio/sour…