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Merge Xtree Outputs Specifications

Process Details

  • Name: merge_xtree_outputs
  • Process UUID: f9319b1ufe5cfnhhykhmh2poqpya54
  • Process Group: short_read_taxonomy

Overview

This process merges XTree coverage files into a single table and performs post-processing to generate relative abundance estimates for taxonomic classification analysis. It consolidates multiple coverage files from XTree taxonomic analysis and applies filtering thresholds to produce cleaned abundance data.

This process is implemented in Bash, which invokes an R script for data merging and post-processing operations.

Key Functionality

  • Coverage File Consolidation: Merges multiple XTree coverage files into a unified dataset
  • Relative Abundance Calculation: Generates relative abundance estimates from coverage data
  • Threshold Filtering: Applies configurable filtering parameters to remove low-abundance taxa
  • Kingdom-Specific Processing: Handles different taxonomic kingdoms (bacterial/archaeal, protozoa/fungi, viral) separately

Input/Output Specification

Inputs

Required Inputs

  • Reference

    • Description: XTree reference file containing taxonomic reference data
    • Format: REF file

  • Coverage

    • Description: XTree coverage files containing taxonomic abundance data
    • Format: COV file

  • Database Mapping

    • Description: Database mapping file for taxonomic classification
    • Format: TXT file

Outputs

  • Output TSV
    • Description: Merged taxonomic abundance table with relative abundance estimates
    • Format: TSV file

Parameters & Settings

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

  • Fraction Parameter for Xtree (hthresh)

    • Description: Fraction parameter for xtree
    • Default value: 0.005

  • Fraction Parameter for Xtree (uthresh)

    • Description: Fraction parameter for xtree
    • Default value: 0.001

  • Xtree Kingdom Options

    • Description: Xtree kingdom options
    • Available options: bacterial_archaeal (default), protozoa_fungi, viral

References & Resources

  • Tool Documentation: Contact the team for details on post_process_xtree.R