CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Abstract

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While 25 this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of 'marker' genes conserved across all bacterial or archaeal 30 genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate, single cell and metagenome derived genomes. CheckM is shown to provide accurate estimates of genome completeness and 35 contamination, and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene-and genome-centric analyses of microbial communities. 40

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

“…Potential contaminant sequences were removed using PRODEGE (Tennessen et al, 2015). The completeness of the genomes within bins was then estimated by counting universal single copy genes using CHECKM (Parks et al, 2014). Binning was also manually curated based on guanine cytosine content, top blast hits and mate pairings.…”

Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion

“…The relatively small but largely complete draft genome recovered from the enrichment culture consists of 1,753,479 nucleotides with a GC content of 36.6%. Analysis of the sequence bin using checkM software (Parks et al, 2015) indicated low level of contamination (2.2%) that is likely from a very similar strain (strain heterogeneity of 100%). One complete rRNA operon (5S, 16S and 23S) and a second copy of the 23S rRNA gene have been identified.…”

Insights into microbial community structure and function from a shallow, simulated CO2‐leakage aquifer demonstrate microbial selection and adaptation

“…Draft genomes were recovered from metagenomic contig datasets using a binning approach based on tetranucleotide frequency with Vizbin (Laczny et al, 2015). Draft genomes were manually curated and genome quality and taxonomy were assessed using Phylopythia (McHardy et al, 2007) and CheckM using the taxonomy_wf command with at least order level specific marker gene sets (Parks et al, 2015). Ribosomal RNA genes in assembled contigs and recovered draft genome bins were predicted using RNAmmer and SSU_Finder from CheckM (Lagesen et al, 2007;Parks et al, 2015).…”

“…Draft genomes were manually curated and genome quality and taxonomy were assessed using Phylopythia (McHardy et al, 2007) and CheckM using the taxonomy_wf command with at least order level specific marker gene sets (Parks et al, 2015). Ribosomal RNA genes in assembled contigs and recovered draft genome bins were predicted using RNAmmer and SSU_Finder from CheckM (Lagesen et al, 2007;Parks et al, 2015). Phylogenetic analysis based on extracted 16S rRNA gene sequences was performed using CLC workbench version 8.5.1.…”