charcoal
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dib-lab
Remove contaminated contigs from genomes using k-mers and taxonomies.
I tried a de novo installation and test of charcoal. I used to use conda for this but moved to mamba over the last two years. Trying to run commands...
Note: PR into https://github.com/dib-lab/charcoal/pull/239 Switch up conda install to what we do over in sourmash
Update sourmash deps to 4.8.4 and snakemake to 7.32.4. Note: sourmash update had to deal with new LineageTuple stuff from https://github.com/sourmash-bio/sourmash/pull/2437. Fixes #237
Trying again to run the Demo from the instructions, but this time, there is something broken with respect to LineagePair from sourmash.lca. I also don't know why in the output...
Hello! Thanks a lot for making this tool available. I ran the demo and analyzed the sample dataset with no issues but when testing charcoal on my own dataset I...
I received this error when I run python -m charcoal run myproject.conf -j 4 report. Any help with that please? Error in rule combine_postprocessing_csv: jobid: 72 output: output.newproject/stage2_summary.csv shell: python...
OS: Ubuntu 20.04, 16 cores, ~ 256 GB RAM. Python: Python 3.9.16 **I got the follow error attempting to run the Demo, following the Quickstart instructions:** git clone https://github.com/dib-lab/charcoal cd...
Following the same process as sourmash-bio/sourmash#2410, we will benchmark the charcoal workflow with [the demo directory](https://github.com/dib-lab/charcoal/tree/latest/demo) and/or the six signatures included in sourmash-bio/sourmash#2410. Suggesting to: 1. Run the demo repo...
https://www.biorxiv.org/content/10.1101/2021.06.22.449360v2
...as alternate/additional contamination analysis per https://github.com/ctb/2022-sourmash-sens-spec/issues/1