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
  • Genome comparison
  • Genome de-replication
  • A dRep based metagenomic workflow
• Installation
  • Using pip
  • Using conda
  • Dependencies
  • CheckM
• Quick Start
  • Dereplication
  • Genome comparison
• Example Output
  • Figures
  • Warnings
  • Other data
• 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
  • Compare
  • Dereplicate
  • Work Directory
  • Genome filtering
  • Warnings
• Advanced Use
  • Accessing Internal Information
  • Using external genome quality information
  • Caching
  • API
  • Troubleshooting checkM
• dRep API
  • drep.d_filter
  • drep.d_cluster
  • drep.d_choose
  • drep.d_analyze
  • drep.WorkDirectory