bio-comparative-genomics-pangenome-analysis
Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building
npx skills add BioTender-max/awesome-bio-agent-skills --skill pangenome-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Panaroo 1.5.1+ (Tonkin-Hill 2020 Genome Biol 21:180), PPanGGOLiN 2.2.0+ (Gautreau 2020 PLoS Comp Biol 16:e1007732), PEPPAN 1.0.5+ (Zhou 2020 GR 30:1667), GET_HOMOLOGUES 25102023+, anvi'o 8.0+ (Eren 2021 Nat Microbiol 6:3), Minigraph-Cactus (Hickey 2024 Nat Biotech 42:663; bundled with Cactus 2.5+), PGGB 0.7.5+ (Garrison 2024 Nat Methods 21:2008), vg 1.59.0+ (Sirén et al 2024 NAR Genom Bioinform 6:lqae001), PanGenie 3.1.0+ (Ebler 2022 Nat Genet 54:518), PGR-TK 0.3.6+ (Chin 2023 Nat Methods 20:1290; cschin/pgr-tk; repo archived April 2026 transitioning to PANGEA), PANGEA (in development by DGI / Diploid Genomics as PGR-TK's successor for pangenome graph exploration + analysis -- check https://github.com/cschin/pgr-tk for current repository pointer), Bakta 1.10.4+ (annotation for input), Roary 3.13.0+ (DEPRECATED; use Panaroo), Scoary 1.6.16+, pyseer 1.3.11+, BUSCO 5.7+, FastTree 2.1.11+, RAxML-NG 1.2+. Python 3.10+ required for Panaroo / PPanGGOLiN. Before using code patterns, verify installed versions match. If versions differ: - CLI: `panaroo --version`; `ppanggolin --version`; `peppan --help`; `cactus-pangenome --help`; `pgg
- Version Compatibility
- Algorithmic Taxonomy
- Decision Tree by Experimental Scenario
- Per-Tool Failure Modes
- Annotation heterogeneity inflating accessory genome
- Tettelin partition class boundary artifacts
- Roary's annotation-error noise (DEPRECATED tool)
- Pangenome graph reference bias (eukaryote)
- Heaps law misapplied
- PGGB memory exhaustion at many genomes
- vg index version mismatch breaking giraffe
- PanGenie genotype false positives in repetitive regions
- Bacterial pangenome with frequent gene-content recombination
- Annotation density variation across genomes
mkdir -p annotated for fa in genomes/*.fa; do bakta --db /path/to/bakta-db --threads 16 \ done panaroo -i annotated/*.gff -o panaroo_out -t 16 \ panaroo_out/gene_presence_absence.csv strains x genes matrix panaroo_out/core_gene_alignment.aln core gene MSA for phylogeny panaroo_out/pan_genome_reference.fa consensus pangenome sequence python tettelin_partition.py \ PPanGGOLiN expects a TSV index: `genome_name<TAB>path/to.gff3` per row
What does the bio-comparative-genomics-pangenome-analysis skill do?
Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pangenome-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.