bio-metagenomics-strain-tracking

name	bio-metagenomics-strain-tracking
description	Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
tool_type	cli
primary_tool	MASH

Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, MetaPhlAn 4.1+, numpy 1.26+, pandas 2.2+, samtools 1.19+, scipy 1.12+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Strain Tracking

"Track bacterial strains across my samples" → Resolve sub-species variation using genome sketching (Mash/sourmash), average nucleotide identity (fastANI), or within-sample strain profiling (inStrain) for outbreak tracking and transmission analysis.

• CLI: mash dist, sourmash compare, fastANI, inStrain profile

Identify and track bacterial strains at sub-species resolution.