| name | instrain |
| description | Strain-level microdiversity and shared-strain detection from metagenomes. Use this skill when working with instrain: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/MrOlm/inStrain. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["strain","microdiversity","snp"] |
| upstream | https://github.com/MrOlm/inStrain |
| stage | strain |
inStrain
Upstream: inStrain
Citation
Olm, M. R. et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat. Biotechnol. 39, 727–736 (2021). https://doi.org/10.1038/s41587-020-00797-0
See also docs/references.md.
Analytical thinking
Species-level profilers (MetaPhlAn, Kraken, sylph) and MAG catalogues do not
resolve within-species SNP microdiversity or prove strain sharing across
samples. inStrain profiles diversity from reads mapped to genomes/MAGs and
detects shared strains with sensitive comparisons.
Requirements for trustworthy results:
- High-quality mapping to dereplicated, preferably high-completeness genomes
- Adequate breadth/depth of coverage (tool filters — report them)
- Not a replacement for species profiling or for ANI catalogue building (
drep /
skani)
Typical order: bin → CheckM2/GUNC → dRep → map reads → inStrain profile →
optional compare for shared strains.
How to run
inStrain profile temp/map/${id}.bam genomes.fa -o temp/instrain/${id} -p 16
Key parameters
| Input | Notes |
|---|
| BAM | To dereplicated references; consistent mapper |
| Coverage / breadth filters | Follow upstream defaults or justify changes |
compare | Shared-strain detection across profiles |
Related skills
bowtie2 · strobealign · drep · skani · coverm · metaphlan ·
tool-selection · metagenomics-workflow
