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Merge Bracken Specifications

Process Details

  • Name: merge_bracken
  • Process UUID: f931wuzl5mjv14tkzribxced6d10cb
  • Process Group: short_read_taxonomy

Overview

This process merges standardized Bracken outputs across all samples in a taxonomic classification analysis. Bracken (Bayesian Reestimation of Abundance with KrakEN) provides species-level abundance estimates from metagenomic sequencing data, and this process consolidates individual sample results into comprehensive summary tables for downstream analysis.

This process is implemented in Bash, which invokes a Python script for data concatenation operations.

Key Functionality

  • Multi-rank Processing: Processes taxonomic data across six taxonomic ranks (species, genus, family, order, class, phylum)
  • Parallel Execution: Runs merging operations for different taxonomic ranks simultaneously to optimize processing time
  • Data Consolidation: Combines individual sample Bracken outputs into unified CSV files for each taxonomic level

Input/Output Specification

Inputs

Required Inputs

  • csvout
    • Description: Individual Bracken CSV output files from taxonomic classification, typically containing abundance estimates for each sample at various taxonomic ranks
    • Format: CSV

Outputs

  • csvout
    • Description: Merged taxonomic abundance tables containing consolidated results across all samples for each taxonomic rank (species, genus, family, order, class, phylum)
    • Format: CSV

Parameters & Settings

This process uses predefined taxonomic ranks and does not require user-configurable parameters.

References & Resources

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