Menu

Individual skill

bio-epidemiological-genomics-pathogen-typing

0upvotes

Assigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR/SeqSero2 Salmonella, SerotypeFinder E. coli, Kaptive Klebsiella, SeroBA pneumococcus, spa+SCCmec S. aureus), and lineage callers (TB-Profiler/Mykrobe barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use when typing bacterial isolates for surveillance or outbreak investigation, choosing between cgMLST allele distance and core-SNP distance for cluster definition, harmonising calls across schemas/database versions, assigning MTBC lineage with the Napier 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with pangolin-data version pinning, or selecting a typing resolution to match the surveillance question.

skills/bioskills/bio-epidemiological-genomics-pathogen-typing/SKILL.md

Read pinned source

Source commit ef85836a0b900799d7d478593080a84d64a86d8c

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
No
Repository scan complete
No
Skill scan complete
No
Observed behavior
Not checked yet
Last checked
Nov 4, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
663
Repository last updated
Nov 8, 2026
License
MIT

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt

## Version Compatibility

Reference examples tested with: mlst 2.23+, chewBBACA 3.3+, SISTR 1.1+, SeqSero2 1.3+, SerotypeFinder 2.0+, Kleborate 3.0+, Kaptive 3.0+, SeroBA 1.0+, PopPUNK 2.7+, pangolin 4.3+ (pangolin-data 1.30+), nextclade 3.8+, tb-profiler 6.2+, mykrobe 0.13+, mash 2.3+, skani 0.2+, snippy 4.6+, snp-dists 0.8+, pandas 2.2+, BioPython 1.84+.

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name`
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
- Pangolin: `pangolin --all-versions` records pangolin + pangolin-data + scorpio + constellations
- Nextclade dataset: `nextclade dataset list --tag latest sars-cov-2`
- chewBBACA schema: schemas are versioned independently; record the schema source AND the schema-fetch date for any published call
- TB-Profiler bundled DB: `tb-profiler list_db` for the WHO catalogue edition currently bundled

If a tool reports an unexpected serovar / lineage / ST, the schema or barcode version is the first thing to check; introspect the installed package and database date before re-running.