Related Tools for Downstream Analysis

The following tools are compatible with both Kraken 1 and Kraken 2. These tools are designed to assist users in analyzing and visualizing Kraken results.

For issues with any of the listed tools, please only open Github issues on their respective pages. Kraken 2's Github page is for Kraken 2 issues only.

Bracken

Bracken allows users to estimate relative abundances within a specific sample from Kraken 2 classification results. Bracken uses a Bayesian model to estimate abundance at any standard taxonomy level, including species/genus-level abundance.

• Website: https://github.com/jenniferlu717/Bracken/
• Function: Abundance estimation from Kraken

KrakenTools

KrakenTools is a suite of tools for downstream analysis with Kraken 2/Bracken results. This suite is continuously evolving and expanding as requested by Kraken/Bracken users.

• Website: https://github.com/jenniferlu717/KrakenTools/
• Functions:
  1. Extract classified sequences for specific taxids
  2. Convert KrakenReport to Krona-compatible text file

Pavian

Pavian has also been developed as a comprehensive visualization program that can compare Kraken 2 classifications across multiple samples.

• Website: https://github.com/fbreitwieser/pavian
• Functions:
  1. Visualize Kraken reports
  2. Compare multiple samples