epidemiological-genomics-pathogen-typing

epidemiological-genomics-pathogen-typing is a Bioinformatics & life sciences skill for AI agents, published by swaruplab in the operon repository on GitHub. Skillspace rates epidemiological-genomics-pathogen-typing C (78/100) and it passed the safety scan; the rating is based on static analysis only.

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 for Salmonella; SerotypeFinder for E. coli; Kaptive K/O for Klebsiella; SeroBA for pneumococcus; spa + SCCmec for S. aureus), and lineage callers (TB-Profiler / Mykrobe Coll-Napier 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 (chewBBACA vs Ridom vs EnteroBase), assigning MTBC lineage with the Napier 2020 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with explicit pangolin-data version pinning, or…

Grade
C
Quality
78 / 100
Safety
Passed
GitHub stars
90

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

This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.

View source on GitHubswaruplab/operon

Our review

Architecture
95 / 100
Maturity
Structured: ships references or scripts
Security scan
No issues found
License
MIT
Adoption
Adopted by 0 other repositories, in 1 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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