cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat
How to install cogeqc?
biomate-ai/biomate-bioconductor-kb/cogeqc
$npx -y skills add biomate-ai/biomate-bioconductor-kb --skill cogeqcInstalls into the current project.
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Run `npx skills use "https://github.com/biomate-ai/biomate-bioconductor-kb" --skill "biomate-ai/biomate-bioconductor-kb/cogeqc"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/biomate-ai/biomate-bioconductor-kb" that are relevant to the current task. Run `npx skills add "https://github.com/biomate-ai/biomate-bioconductor-kb"` and select the relevant skills, then follow their instructions.
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