Checkm Sh Specifications

Process Details

• Name: checkm_sh
• Process UUID: f931dd5iyz3wftcl06cyb1km458dlp
• Process Group: MAG-qc

Overview

This process runs CheckM's lineage_wf tool to assess the quality of metagenome-assembled genomes (MAGs). CheckM provides a comprehensive assessment of genome completeness and contamination by analyzing the presence of lineage-specific marker genes. This is essential for evaluating the quality of assembled genomes from metagenomic data before downstream analyses.

This process is implemented in Bash.

Key Functionality

• Genome Quality Assessment: Evaluates completeness and contamination levels of metagenome-assembled genomes using lineage-specific marker genes
• Lineage-Specific Analysis: Automatically determines the most appropriate reference lineage for each genome based on phylogenetic placement
• Comprehensive Reporting: Generates detailed quality metrics including completeness percentages, contamination levels, and strain heterogeneity estimates

Input/Output Specification

Inputs

Required Inputs

• Fasta File

  • Description: Set of metagenome-assembled genome sequences in FASTA format
  • Format: fasta

• Diamond Database

  • Description: CheckM reference database in Diamond format containing marker gene sequences
  • Format: dmnd

Outputs

• Output File TSV
  • Description: Tab-separated values file containing CheckM quality assessment results including completeness, contamination, and other genome statistics
  • Format: tsv

Parameters & Settings

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

References & Resources

• Tool Documentation: Contact the team for details on CheckM lineage workflow implementation
• Related Papers: Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., and 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