New Module: OMArk - Githubissues

NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

https://www.earthbiogenome.org/

GNU General Public License v3.0

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New Module: OMArk #54

Closed gbdias closed 9 months ago

gbdias commented 9 months ago

Which tool should be included? OMArk. https://github.com/DessimozLab/OMArk

How is it used?

# installation
pip install omark
# download full database
wget https://omabrowser.org/All/LUCA.h5
# run search and benchmark
omamer search --db LUCA.h5 --query my_proteome.fa --out my_proteome.omamer --nthreads 10
omark -f my_proteome.omamer -d LUCA.h5 -o results

Which workflow should it be included in? Quality control.

gbdias commented 9 months ago

Closing since I realised this might not be needed for the EBP workflow as it is geared towards annotation evaluation rather than assembly evaluation.

mahesh-panchal commented 9 months ago

You can add it as an issue here: https://github.com/NBISweden/pipelines-nextflow Just say if it needs to be a workflow of it's own. Check the Mermaid diagram.