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Hello,
If I wanted to do exact k-mer comparisons between genome assemblies could I simple use `sourmash sketch` with `scaled=1`?
Is this a stupid thing to do?
I have a limited set of bacterial…
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Still needs work, esp around talking about what sourmash is actually doing. But first pass!
Charcoal identifies and removes contamination in metagenome-assembled genomes using k-mer based methods.
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This is an update of and replacement for https://github.com/dib-lab/sourmash/issues/999, which raised a lot of issues around how we were doing protein k-mer calculations.
This issue is being update…
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Dear sourmash team,
I've recently attempted to create a minimal test dataset and encountered an error when using `sourmash gather`.
Specifically, it raises an `AssertionError`.
I think that t…
vmikk updated
8 months ago
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I was wondering if it was worth looking at within signature differences to get an idea of the diversity of hashes? i.e using Jaccard, Hammings or Lenvestein metrics.
I need to check my understanding…
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Use tools from spacegraphcats to do the indexing https://github.com/spacegraphcats/spacegraphcats/issues/273
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```
mprof run sourmash gather SRR606249.k31.sig.gz /group/ctbrowngrp/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.zip --save-prefetch-csv p2.csv -o g2.csv
mprof plot -o ~/transfer/gather.p…
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not sure this is the right place to ask, but: is there a ball park estimate of how many reads/ bases are at least required to reliably identify an isolate of some bacterium? in terms of coverage, 1x s…
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opening a new issue to focus on *minimal* wording...
related to #3, and [this comment](https://github.com/dib-lab/2020-paper-sourmash-gather/issues/3#issuecomment-717248822) specifically. quotes fr…
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despite https://github.com/dib-lab/sourmash/issues/1571, the problems in #1552 continued after using the new `remove_many` implementation until I refactored the enclosing script in #1613.
The follo…