InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification
Source code is available on GitHub.
See links to the left for Installation instructions
Bugs reports and feature requests can be submitted through GitHub.
- Glossary & FAQ
- Important concepts
- 1. An overview of inStrain and the data it generates
- 2. Representative genomes and their utility
- 3. Picking and evaluating representative genomes
- 4. Establishing and evaluating genome databases
- 5. Handling and reducing mis-mapping reads
- 6. Detecting organisms in metagenomic data.
- 7. Strain-level comparisons and popANI.
- 8. Thresholds for determining “same” vs. “different” strains.
- 9. Importance of representative genomes when calculating popANI
- 10. Using inStrain for gene-based functional analysis
- 11. Reducing inStrain resource usage
- User Manual
- Expected output
- Raw data access and API