Pass work between ORS skills with a Material Passport — a structured JSON envelope that captures inputs, outputs, decisions, and provenance so a downstream skill can resume without re-deriving context. Use when one skill produces output that another skill must consume, especially across category boundaries (e.g. analysis → writing, sequencing → statistics).
Discover and maintain `## Cross-references` between ORS skills. Given a new or edited skill, suggest related skills (same category, shared tags, complementary workflows). Verify all xref slugs resolve to existing SKILL.md files. Use when adding a new skill, when sibling skills move, or when an audit reveals dangling xrefs.
7-mode AI failure-mode checklist applied before publishing any ORS artifact (skill, manuscript section, dataset card, agent output). Catches: fabricated citations, silent failures, scope creep, missing provenance, unsupervised writes, version drift, hallucinated APIs. Use as the final pass before any 'publish', 'release', 'merge', or 'finalize' action.
Version, changelog, and marketplace workflow for ORS skills. Semver discipline, breaking-change protocol, marketplace.json update, README refresh, and the v0.X.Y → v1.0.0 graduation criteria. Use when bumping a skill version, publishing a release, or upgrading the ORS package version.
Author a new ORS skill from scratch using the v0.4.0 schema. Produces a valid SKILL.md (frontmatter + metadata + sections) following spec/skill-format.md, guided by spec/author-guide.md, validated by scripts/validate-skills.py. Use when a user says 'add a new skill', 'create a skill for X', or 'I want to contribute a skill'.
Process many FASTA/FASTQ/GenBank files in batch — merge, split, convert, summarize, organize — using Biopython 1.83+.
Align short reads to a reference with Bowtie2 — the standard aligner for ChIP-seq, ATAC-seq, and other short-fragment applications where sensitivity for short indels matters less than speed.
Align Illumina short reads to a reference genome with BWA-MEM — including index, MEM algorithm, paired-end, alt-contig handling, and 2026 best practices.