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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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as of the merge of #160, charcoal now performs the following steps -
1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95
2. download genomes and per…
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Hello !
Sorting the output CSV for ````sourmash compare```` would make results analysis easier.
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I'm running some metatranscriptomic samples through grist, and getting very little classified with the below parameters. I'm wondering if I should lower the threshold below 5e3, and/or if I should use…
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!?!?!
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@taylorreiter mentioned the new [`datasets`](https://www.ncbi.nlm.nih.gov/datasets/docs/about-ncbi-datasets/) tool from NCBI on Slack, and the downloaded file is a zip file in the [BDBag](https://gith…
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Dumping this here so it's recorded somewhere. This reads in a signature with multiple minhashes, output by gather using the flag `--save-matches`.
```
library(dplyr)
library(rjson)
sig_json
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I put together a notebook for tracking workflow using sourmash here:
https://github.com/bioinfonm/bat_metagenomics_2016/blob/master/python_code/sourmash_CAVE_bat_metagenomes.ipynb
Change log:
pylab.s…
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With the merge of `StandaloneManifestIndex` https://github.com/sourmash-bio/sourmash/pull/1891 and `sourmash sig check` https://github.com/sourmash-bio/sourmash/pull/1907, and the advent of `sourmash …
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Hi! I'm using `sourmash signature kmers` to extract kmers and a fasta from a signature of hashes of interest and the original fasta file.
My command:
```
sourmash sig kmers --signatures --sequ…