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@mr-eyes has been working steadily on using kspider ([docs](https://dib-lab.github.io/kSpider/) and [repo](https://github.com/dib-lab/kspider)) to cluster many large collections of k-mers, and has ach…
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from STAMPS 2022 - https://hackmd.io/vYaK2UngTWSkKmcpQMP6NA
associated presentations and tutorials -
[taylor on assembly and binning](https://github.com/mblstamps/stamps2022/blob/main/assembly_a…
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right now it's not really specified anywhere 😆
```
ident,superkingdom,phylum,class,order,family,genus,species
GCF_014075335.1,d__Bacteria,p__Proteobacteria,c__Gammaproteobacteria,o__Enterobacteral…
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Ran sourmash gather on pig gut metagenomes against gtdbtk. Assembled MAGs from the metagenomes, then reran gather against gtdbtk + newly assembled MAGs. For most of the metagenomes, total % coverage o…
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For now, if identifiers are found in multiple lineage spreadsheets, the reported lineage will be from the last spreadsheet input, as reading each will update the taxonomy dictionary, overwriting prior…
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looking at the code, probably, yes! #1837 would help with this.
background and motivation: for large .sig.gz files, it is annoying to load all of the JSON if you just want specific moltypes/ksizes/…
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similar to #829
probably should use new `sourmash_args.load_file_as_signatures` function re #1059
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Hi, a big thank you to the developers of this useful and versatile tool. I am using sourmash to detect and remove undesired prokaryotes from WGS datasets in my de-novo assembly pipeline of prokaryotic…
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For now, `load_query_signature` does an iterative search for md5 matches across all signatures. We can/should change this to use `db.select(...)` with picklists and/or manifests, so as to take advanta…
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Random gemisch / brainstorming about an opportunity I have to give a more in depth tech talk on sourmash at JGI in early May 2020. What should I cover?
An incomplete list of potential tech-y topics…