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Xtree Specifications

Process Details

  • Name: xtree
  • Process UUID: f931gfyxt62vwzagonjuvcorxur5tg
  • Process Group: short_read_taxonomy

Overview

The Xtree process is designed to classify the microbial community composition and estimate coverage from sequencing data. This tool provides taxonomic classification capabilities for microbiome analysis, enabling researchers to identify and quantify microbial species present in their samples while determining the sequencing depth coverage for each identified organism.

This process is implemented in Bash, which invokes the Xtree classification tool for microbial community analysis.

Key Functionality

  • Taxonomic Classification: Identifies and classifies microbial species present in the sequencing data using a reference database
  • Coverage Estimation: Calculates sequencing coverage metrics for each identified microbial organism
  • Community Composition Analysis: Provides comprehensive profiling of the microbial community structure and abundance

Input/Output Specification

Inputs

Required Inputs

  • FASTQ Set

    • Description: Collection of sequencing read files containing the sample data to be analyzed
    • Format: FASTQ

  • Xtree Database

    • Description: Reference database file used for taxonomic classification of microbial sequences
    • Format: XTR

Outputs

  • Reference

    • Description: Reference alignment and classification results showing taxonomic assignments
    • Format: REF

  • Coverage

    • Description: Coverage statistics and depth information for identified microbial organisms
    • Format: COV

Parameters & Settings

This process uses default parameters optimized for microbial community analysis. The tool automatically utilizes available CPU threads for parallel processing and applies redistribution algorithms for improved classification accuracy.

References & Resources

  • Tool Documentation: Contact the team for details on the Xtree classification tool
  • Related Papers: Xtree: A tool for microbial taxonomic classification and coverage estimation from short-read sequencing data