InStrain
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.
Publication is available in Nature Biotechnology and on bioRxiv
See links to the left for Installation instructions
Bugs reports and feature requests can be submitted through GitHub.
InStrain was developed by Matt Olm and Alex Crits-Christoph in the Banfield Lab at the University of California, Berkeley.
Contents
- Installation
- 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
- Tutorial
- User Manual
- Expected output
- Raw data access and API
- Benchmarks
- Acknowledgements