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DAS Tool Specifications

Process Details

  • Name: DAS Tool
  • Process UUID: f931ra3jhdfydn4fvi50xgiaxbkgqn
  • Process Group: Binning

Overview

DAS Tool is a bin refinement process designed to improve the quality of genome bins generated by multiple binning tools in metagenomics workflows. The process integrates results from various binning algorithms to produce a refined set of high-quality bins by selecting the best bins from each tool and resolving conflicts between overlapping bins.

This process is implemented in Bash, which is executed within a Groovy-based workflow script using the DAS Tool containerized application.

Key Functionality

  • Multi-tool Integration: Combines binning results from up to six different binning tools (MetaBAT2, MaxBin2, MetaBinner, SemiBin2, CONCOCT, and VAMB)
  • Quality-based Selection: Evaluates and selects the highest quality bins based on completeness and contamination metrics
  • Conflict Resolution: Resolves overlapping bin assignments by choosing the best representative for each genomic region
  • Comprehensive Output: Generates refined bins, unbinned contigs, and detailed evaluation metrics

Input/Output Specification

Inputs

Optional Inputs

  • Input Directory
    • Description: Directory containing binning results from various binning tools (can accept multiple directories for different binning outputs)
    • Format: Directory

Outputs

  • Log Output

    • Description: Process execution log containing detailed information about the refinement process and file listings
    • Format: Log file (.log)

  • Output Directory

    • Description: Directory containing refined bins, evaluation metrics, and unbinned contigs organized by sample
    • Format: Directory

Parameters & Settings

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

  • DAS Tool Threshold
    • Description: Enter the threshold value for bin refinement
    • Default value: 0.5

References & Resources

  • Tool Documentation: Contact the team for details on DAS Tool containerized application
  • Related Papers: Sieber, C.M.K., Probst, A.J., Sharrar, A. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1