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
• Installation
  • Using pip
  • Dependencies
  • pyenv
• Quick Start
  • De-replication
  • Genome comparison
• Example Output
  • Figures
  • Warnings
  • Other data
• Choosing parameters
  • What defines genomes as being “same”?
  • What is the minimum genome completeness allowed in analysis?
  • The Rest
• Module Descriptions
  • Work Directory
  • Compare and Dereplicate
  • Filter
  • Cluster
  • Choose
  • Analyze
  • Evaluate
  • Bonus
• Advanced Use
  • Accessing Internal Information
  • Using external genome quality information
  • Caching
  • API
• dRep API
  • drep.d_filter
  • drep.d_cluster
  • drep.d_choose
  • drep.d_analyze
  • drep.WorkDirectory