roary-pangenome
byjaechang-hits· 57 skills
Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with -e), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.
How to install roary-pangenome?
jaechang-hits/sciagent-skills/roary-pangenome
$npx -y skills add jaechang-hits/sciagent-skills --skill roary-pangenomeInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/jaechang-hits/sciagent-skills" --skill "jaechang-hits/sciagent-skills/roary-pangenome"` 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/jaechang-hits/sciagent-skills" that are relevant to the current task. Run `npx skills add "https://github.com/jaechang-hits/sciagent-skills"` and select the relevant skills, then follow their instructions.
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