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MetaBAT2 Specifications

Process Details

  • Name: MetaBAT2
  • Process UUID: f9311s47dc09lgqbkb9ksd6a6m7m46
  • Process Group: Binning

Overview

MetaBAT2 is a binning tool designed for generating metagenome-assembled genomes (MAGs) from short-read sequencing data. This process clusters assembled contigs into bins based on tetranucleotide frequency patterns and differential coverage across multiple samples, enabling the reconstruction of individual microbial genomes from complex metagenomic datasets.

This process is implemented in Bash, which utilizes the MetaBAT2 algorithm for contig binning and genome reconstruction.

Key Functionality

  • Contig Binning: Groups assembled contigs into bins representing individual microbial genomes based on composition and coverage patterns
  • Coverage Analysis: Utilizes depth information from mapping data to improve binning accuracy through differential coverage
  • Quality Filtering: Applies minimum contig length thresholds to focus on contigs suitable for genome reconstruction
  • Unbinned Contig Recovery: Optionally retains contigs that could not be assigned to any bin for further analysis

Input/Output Specification

Inputs

Required Inputs

  • inputDir
    • Description: Directory containing prepared binning data including assembled contigs and coverage information
    • Format: directory

Outputs

  • logFile

    • Description: Process execution log containing binning statistics and runtime information
    • Format: log

  • outputDir

    • Description: Directory containing the binned contigs organized into separate genome bins
    • Format: directory

Parameters & Settings

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

  • Minimum Contig Length
    • Description: Write the minimum expected contig length for MaxBin2 to work on. The value should be an integer!
    • Default value: 2500

References & Resources

  • Tool Documentation: Contact the team for details on metabat2
  • Related Papers: Kang, D.D., Li, F., Kirton, E. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019). https://doi.org/10.7717/peerj.7359