bio-comparative-genomics-whole-genome-alignment

bio-comparative-genomics-whole-genome-alignment is a Bioinformatics & life sciences skill for AI agents, published by BioTender-max in the awesome-bio-agent-skills repository on GitHub. Skillspace rates bio-comparative-genomics-whole-genome-alignment C (79/100) and it passed the safety scan; the rating is based on static analysis only.

Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

Grade
C
Quality
79 / 100
Safety
Passed
GitHub stars
115

Unproven: rated by static analysis only, not yet compared head-to-head.

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View source on GitHubBioTender-max/awesome-bio-agent-skills

Our review

Architecture
97 / 100
Maturity
Structured: ships references or scripts
Security scan
No issues found
License
Not declared. Check the repository before reusing it.
Adoption
Adopted by 0 other repositories, in 2 collections

Not checked yet

  • Not judged on the rubric yet (not a contender in its category)
  • No blind task eval yet
  • Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
  • Sibling files (scripts, references) not fetched; security scan covers SKILL.md only

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