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Standardize Xtree Specifications

Process Details

  • Name: standardize_xtree
  • Process UUID: f931k06wivouis0734tzl4o3f5m5es
  • Process Group: short_read_taxonomy

Overview

This process converts XTree taxonomic classification output to a standardized format that can be consistently used across different taxonomic ranks and downstream analyses. It transforms the raw XTree results into a clean, structured format suitable for comparative taxonomic studies and reporting.

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

Key Functionality

  • Format Standardization: Converts XTree output files to a consistent CSV format for downstream analysis
  • Taxonomic Rank Processing: Handles taxonomic data across different hierarchical levels using NCBI taxonomy references
  • Threshold Filtering: Applies user-defined fraction thresholds to filter taxonomic assignments based on confidence levels

Input/Output Specification

Inputs

Required Inputs

  • outFileTSV

    • Description: XTree output file containing taxonomic classification results
    • Format: TSV (Tab-separated values)

  • dump

    • Description: NCBI taxonomy dump file providing taxonomic hierarchy and reference data
    • Format: DMP (NCBI dump format)

Outputs

  • csvout
    • Description: Standardized taxonomic classification results in a consistent format for downstream analysis
    • Format: CSV (Comma-separated values)

Parameters & Settings

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

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

References & Resources

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