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code in #40 could benefit from making `SeqToHashes` less opaque over in sourmash.
Some ideas:
* simple and lightweight: provide access to `kmer_index` per https://github.com/oxli-bio/oxli/pull/4…
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https://github.com/sourmash-bio/sourmash_plugin_branchwater?tab=readme-ov-file
sourmash plugin pour utilisation en multithread. En gros, en ce moment la fonction Sourmash gather n'est pas paralléli…
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How fast can we make kmer counting in Rust?
@ctb, are there examples of this from Sourmash or other libraries?
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Once https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/408 is merged, there's no real reason to have this plugin around - so, deprecate following the procedure in https://github.com/sou…
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it's kind of cool 😆
see https://github.com/sourmash-bio/sourmash_plugin_branchwater/blob/a45163eff0951e430911d071b3957efe6c3c40e2/src/mastiff_manysearch.rs#L57
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I encountered an issue while running the BACANNOT pipeline, specifically with the GET_NCBI_GENOME process. Here is the error message I received:
```console
ERROR ~ Error executing process > 'BACA…
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In https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/381, we found a problem when using RocksDB inverted indexes with zip files.
Starting from https://github.com/sourmash-bio/sour…
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A common use of kmer counters is to dump kmers and their counts to a text file that can be used in other tools. To do this we need to track hash to kmer pairs.
Suggested solution:
Init `KmerCoun…
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This command will stream the fasta file (whether SE or PE) to sourmash for sketching.
```sh
fasterq-dump --fasta-unsorted ${sra_accession} --stdout | sourmash sketch dna - ....
```
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Hi!
I am grying out this tool now. I installed via conda, and am using it on a slurm run cluster with srun. Have asked for 10 cpus. I have a file list containing 8 plasmid fasta seqs. The plasmids …