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Checkm Cov Specifications

Process Details

  • Name: checkm_cov
  • Process UUID: f9316wzfhhgwv6y4nfesutqsnt8ajd
  • Process Group: MAG-qc

Overview

This process computes genome coverage statistics for Metagenome-Assembled Genomes (MAGs) using CheckM's coverage tool. It leverages indexed BAM files to calculate coverage metrics that are essential for assessing the quality and completeness of assembled genomes in metagenomic studies.

This process is implemented in Bash, which invokes CheckM's coverage module for genome coverage analysis.

Key Functionality

  • Coverage Calculation: Computes comprehensive coverage statistics for MAGs using aligned sequencing reads
  • BAM File Processing: Utilizes indexed BAM files containing aligned reads for accurate coverage computation
  • Multi-threading Support: Leverages available CPU threads for efficient processing of large genomic datasets

Input/Output Specification

Inputs

Required Inputs

  • fastaFile

    • Description: FASTA file(s) containing the assembled genome sequences (MAGs) for coverage analysis
    • Format: FASTA

  • outputDir

    • Description: Directory where CheckM coverage results and intermediate files will be stored
    • Format: Directory

Outputs

  • outputFileTSV
    • Description: Tab-separated values file containing detailed coverage statistics for each genome, including coverage depth, breadth, and other quality metrics
    • Format: TSV

Parameters & Settings

No user-configurable parameters are available for this process in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on CheckM coverage analysis
  • Related Papers: Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., & Tyson, G.W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25(7), 1043-1055. doi:10.1101/gr.186072.114