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. Although 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 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 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.

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C 1 Compound Oxidation

“…The latter relied on read recruitment with the Bowtie 2 program (default settings) (33) using 10 million paired-end reads from offshore spring surface and bottom water samples and summer bottom water samples. Analysis was performed with the CheckM tool to assess the completeness and purity of the final Chloroflexi CL500-11-LM sequence bin (34). We also performed a CheckM analysis on the genome of the closest sequenced isolate, Anaerolinea thermophila UNI-1 (35).…”

Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N -Nitroglycine by Variovorax sp. Strain JS1663

“…3.0) and CheckM (ver. 1.0.5) software assessed de novo genome assembly quality (59,60). The permanent draft assembly contained 140 contigs comprising 7,324,361 bp, with an N 50 of 115,706 bp, an L 50 of 20 contigs, and a GϩC content of 68%.…”

Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens

“…Due to short scaffolds and the paucity of reference data, we cannot estimate the reliability of scaffold assembly in mitochondrial genes and SCGs, but this may be more problematic with closely related species. Such assembly problems are considered of minor importance in prokaryote metagenomes (Wrighton et al 2012;Parks et al 2015) because of a single circular chromosome, lower proportion of repeats, more rapid evolution and more relaxed definition of species/OTUs at 97% SSU similarity (Mende et al 2013). …”