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DAS Tool Prep Specifications

Process Details

  • Name: DAS Tool Prep
  • Process UUID: f931t9fs8z5hh4855mm5kkjbp4x5k2
  • Process Group: Binning

Overview

DAS Tool Prep is a preprocessing step for binning refinement that prepares genomic bin data for analysis with DAS_Tool. This process organizes bin files, extracts the main assembly FASTA file, and generates the required contig-to-bin mapping file that DAS_Tool needs for bin quality assessment and refinement.

This process is implemented in Bash, which invokes the Fasta_to_Contig2Bin.sh script for generating contig-to-bin mappings.

Key Functionality

  • Bin File Organization: Copies and organizes genomic bin files into a structured directory format
  • Assembly Extraction: Identifies and extracts the main assembly FASTA file from the bin collection
  • Contig Mapping Generation: Creates a tab-separated file mapping contigs to their respective bins using the Fasta_to_Contig2Bin.sh utility

Input/Output Specification

Inputs

Required Inputs

  • Input Directory
    • Description: Directory containing genomic bin files in FASTA format, including the main assembly file
    • Format: Directory

Outputs

  • Output Directory
    • Description: Structured directory containing organized bin files, extracted assembly FASTA, and contig-to-bin mapping file ready for DAS_Tool analysis
    • Format: Directory

Parameters & Settings

This process uses automated parameter detection and does not require user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on Fasta_to_Contig2Bin.sh
  • 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