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Contig Depth Calc Specifications

Process Details

  • Name: ContigDepthCalc
  • Process UUID: f9311t5lj7qt74com3e9nwjfz1rijo
  • Process Group: Binning

Overview

ContigDepthCalc calculates contig depths for multiple metagenomic binning tools including metabat2, maxbin2, and metabinner. This process prepares coverage depth files that are essential for genome binning algorithms to group contigs into metagenome-assembled genomes (MAGs) based on coverage patterns and sequence composition.

This process is implemented in Bash, utilizing the MetaBAT2 toolkit's jgi_summarize_bam_contig_depths utility for depth calculations.

Key Functionality

  • Coverage Depth Calculation: Computes contig coverage depths from BAM alignment files using MetaBAT2's depth calculator
  • Multi-tool Compatibility: Generates depth files with appropriate formatting for metabat2, maxbin2, and metabinner binning tools
  • Conditional Processing: Selectively calculates depths only for the binning tools that will be used in downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • Input Directory
    • Description: Directory containing BAM alignment files with sorted alignments of metagenomic reads to assembled contigs
    • Format: Directory

Outputs

  • Output Directory

    • Description: Directory containing calculated depth files for each specified binning tool and processed alignment data
    • Format: Directory

  • Log Output

    • Description: Process execution log containing depth calculation progress and file listings
    • Format: Log file

References & Resources

  • Tool Documentation: Contact the team for details on MetaBAT2 depth calculation utilities
  • Related Papers: Kang, D. D., Li, F., Kirton, E., Thomas, A., Egan, R., An, H., & Wang, Z. (2019). MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ, 7, e7359.