CheckM

CheckM assesses genome completeness and contamination for genomes recovered from isolates, single cells, or metagenomic datasets to enable robust biological inference from draft genomes.

Key Features:

• Phylogenetically informed marker gene set: Uses a comprehensive set of marker genes specific to the phylogenetic position of a genome within a reference tree.
• Marker collocation analysis: Leverages information about the collocation of marker genes to refine evaluations of genome content.
• Completeness and contamination estimates: Provides quantitative estimates of genome completeness and contamination levels.
• Data-type applicability: Applies to genomes derived from isolates, single cells, and metagenomic assemblies.
• Validation on synthetic and real datasets: Demonstrated on synthetic data and a diverse array of isolate-, single-cell-, and metagenome-derived genomes.
• Error detection in public genomes: Identifies a wide range of errors affecting publicly available isolate genomes.
• Assessment of quality variability: Reveals variability in the quality of genomes obtained from single-cell and metagenomic sources.
• Objective genome quality metric: Proposes an objective measure of genome quality to support downstream gene- and genome-centric analyses.

Scientific Applications:

• Draft genome quality assessment: Assessing draft genomes to support robust biological inferences from incomplete assemblies.
• Microbial community analyses: Selecting genomes suitable for gene- and genome-centric analyses of microbial communities.
• Public database quality control: Detecting and characterizing errors in publicly available isolate genomes for database curation.
• Comparative quality evaluation: Evaluating variability in genome quality across single-cell and metagenomic datasets.

Methodology:

Places genomes within a reference phylogenetic tree and uses phylogenetically specific marker gene sets and marker collocation information to estimate genome completeness and contamination.