dRep¶
Rapid and accurate comparison and de-replication of microbial genomes¶
The publication is available at ISME and an open-source pre-print is available on bioRxiv.
Source code is available on GitHub.
See links to the left for Installation and Quick Start instructions
Comments and suggestions can be sent to Matt Olm
Bugs reports and feature requests can be submitted through GitHub.
Contents¶
- Overview
- Installation
- Quick Start
- Example Output
- Important Concepts
- 1. Choosing an appropriate secondary ANI threshold
- 2. Minimum alignment coverage
- 3. Choosing representative genomes
- 4. Using greedy algorithms
- 5. Importance of genome completeness
- 6. Oddities of hierarchical clustering
- 7. Overview of genome comparison algorithms
- 8. Comparing and dereplicating non-bacterial genomes
- User manual
- Advanced Use
- dRep API