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Standardize Bracken Specifications

Process Details

  • Name: standardize_bracken
  • Process UUID: f9318xpd64g2h2ao0if3yvr6dd07h0
  • Process Group: short_read_taxonomy

Overview

This process converts Bracken taxonomic classification output files to a standardized CSV format that can be consistently used across different taxonomic ranks and downstream analyses. Bracken (Bayesian Reestimation of Abundance with KrakEN) produces species-level abundance estimates from Kraken2 classifications, and this standardization step ensures uniform formatting for comparative analyses and visualization.

This process is implemented in Bash, which invokes a Python script for the data standardization and filtering operations.

Key Functionality

  • Format Conversion: Transforms Bracken TSV output files into standardized CSV format
  • Abundance Filtering: Applies minimum relative abundance thresholds to filter out low-abundance taxa
  • Batch Processing: Processes multiple Bracken output files simultaneously using parallel execution
  • Directory Organization: Creates organized output directory structure for standardized results

Input/Output Specification

Inputs

Required Inputs

  • Bracken Output Files
    • Description: TSV files containing taxonomic abundance estimates generated by Bracken
    • Format: TSV (Tab-separated values)

Outputs

  • Standardized Taxonomic Data
    • Description: Standardized CSV files containing filtered taxonomic abundance data in a consistent format across samples
    • Format: CSV (Comma-separated values)

Parameters & Settings

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

  • Minimum Relative Abundance
    • Description: Threshold for filtering taxa based on relative abundance to remove low-abundance classifications
    • Default value: Configurable via min_rel_abund parameter

References & Resources

  • Tool Documentation: Contact the team for details on standardize_bracken.py
  • 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