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phiweger
Finding prophage regions in bacterial genomes using brute force
Hi :) After installing and downloading the test data and databases the workflow seems to freeze at uv:search_protein_db (stops for hours, several times tried). ``` nextflow run main.nf --standalone --results...
when using a "new" version (1.x) https://bitbucket.org/berkeleylab/checkv/src/master/ ```bash diamond makedb --in checkv_reps.faa --db checkv_reps ```
Search a DNA database (metagraph) for CRISPR fragments extracted via minced (wrapped by prokka) and custom parsing.
First off - thanks for this tool! i ran the workflow on the test dataset with no problems, but I've been trying to test it on some genomes we sequenced,...
The db that is downloaded has ~23 GB. Thus, it would be good to add a comment about this to the README (and maybe even the download script as a...
standalone: - phastaf - phigaro - phispy - probably somebody has thrown a neural net at the problem webservices: - phaster2 - BGI tool