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DAS Output Collector Specifications

Process Details

  • Name: DAS Output Collector
  • Process UUID: f9312m4y41ju7p9z6aesswkoi219fq
  • Process Group: Binning

Overview

The DAS Output Collector is a specialized process designed to collect and organize output files from DAS Tool (a method for genome-resolved metagenomics that optimizes assemblies by integrating results from multiple binning algorithms). This process systematically processes DAS Tool output directories, extracts relevant binning results, and reorganizes them into a standardized directory structure for downstream analysis.

This process is implemented in Bash, executed within a Groovy workflow framework.

Key Functionality

  • Directory Processing: Scans and processes DAS Tool output directories containing binned genome assemblies
  • File Organization: Creates organized directory structures based on sample names derived from DAS Tool output naming conventions
  • Bin Collection: Copies and consolidates genome bins from DAS Tool results into sample-specific directories
  • Output Standardization: Ensures consistent file organization for downstream metagenomics analysis workflows

Input/Output Specification

Inputs

Required Inputs

  • Input Directory
    • Description: Directory containing DAS Tool output files and binned genome assemblies
    • Format: Directory

Outputs

  • FASTA Files
    • Description: Organized genome bin sequences in FASTA format, structured by sample
    • Format: FASTA

Parameters & Settings

No user-configurable parameters are available for this process. The process automatically detects and processes DAS Tool output based on standard naming conventions.

References & Resources

  • Tool Documentation: Contact the team for details on the DAS Tool output processing implementation
  • 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