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shakedna1 / wspc_rep

MIT License
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GUI required? #30

Open nick-youngblut opened 1 year ago

nick-youngblut commented 1 year ago

According to the docs:

Use PATRIC's Genome Annotation Service: https://patricbrc.org/app/Annotation.

For detailed instructions, Follow the instructions under the PATRIC genome annotations service documentation: https://docs.patricbrc.org/user_guides/services/genome_annotation_service.html

Download the resulting "Taxonomy name + label".txt file (click on view, then download. "Taxonomy name + label" is the genome name).

If you wish to create a merged *.fasta file for number of genomes, the column "pgfam" will be used for pgfam extraction.

So the user is expected to upload, analyze, and download each genome in order to get the pgfam gene info? If this is the only way to get the required input, then the usability of wspc is quite limited. The user must only have a small number of genomes (no large bioinformatics projects or pipelines), so generally someone who doesn't do much bioinformatics, but the user must still know how to use the command line.

WSPC looked promising, but the manual gene annotation via https://patricbrc.org/app/Annotation is a deal-breaker.

dinasv commented 1 year ago

Hello Nick Youngblut, You can also use RASTtk for bulk annotation https://www.bv-brc.org/docs//cli_tutorial/rasttk_getting_started.html