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Bracken Specifications

Process Details

  • Name: bracken
  • Process UUID: f931j7qbp4jnv40krtkr2hno40ufc9
  • Process Group: short_read_taxonomy

Overview

Bracken (Bayesian Reestimation of Abundance with KrakEN) refines Kraken2's taxonomic classification output to provide more accurate estimates of relative abundance at various taxonomic ranks. This process addresses the limitation of Kraken2 where reads assigned to higher taxonomic levels may actually belong to lower, more specific taxa, thereby improving the precision of microbial community profiling.

This process is implemented in Bash.

Key Functionality

  • Abundance Reestimation: Uses Bayesian methods to redistribute reads from higher taxonomic levels to more specific taxa based on the database composition
  • Multi-rank Analysis: Generates abundance estimates across multiple taxonomic ranks including species, genus, family, order, class, and phylum
  • Parallel Processing: Executes abundance estimation for different taxonomic ranks simultaneously to improve computational efficiency

Input/Output Specification

Inputs

Required Inputs

  • Kraken Database

    • Description: Pre-built Kraken2 database containing reference genomes and taxonomic information
    • Format: kraken

  • Kraken2 Output File

    • Description: Tab-separated file containing taxonomic classification results from Kraken2 analysis
    • Format: tsv

Outputs

  • Abundance Estimates

    • Description: Tab-separated files containing refined abundance estimates for each taxonomic rank
    • Format: tsv

  • Log Files

    • Description: Process execution logs and statistical summaries from Bracken analysis
    • Format: out

  • Output Directory

    • Description: Directory containing all Bracken results organized by taxonomic rank
    • Format: directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Read Length
    • Description: The read length of the data
    • Default value: 100

References & Resources

  • Tool Documentation: Contact the team for details on bracken
  • Related Papers: Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. https://doi.org/10.7717/peerj-cs.104