What it does

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

This command produces a number of plots for assessing the quality of genome bins. Here we describe each of these plots and provide an example.

• gc_plot: Provides a 3 pane plot suitable for assessing the GC distribution of sequences within a genome bin. The first pane is a histogram of the number of non-overlapping 5 kbp windows with a give percent GC. A typical genome will produce a unimodal distribution. The second pane plots each sequence in the genome bin as a function of its deviation from the average GC of the entire genome (x-axis) and sequence length (y-axis). The dashed red lines indicate the expected deviation from the mean GC as a function of length. This expected deviation is pre-calculated from a set of trusted reference genomes and the percentile plotted is provided as an argument to this command. A good default value to use for this distribution parameter is 95.
• coding_plot: Provides a plot analogous to the gc_plot suitable for assessing the coding density of sequences within a genome bin.
• tetra_plot: Provides a plot analogous to the gc_plot suitable for assessing the tetranucleotide signatures of sequences within a genome bin. The Manhattan distance is used for determine the different between each sequence's tetranucleotide signature and the tetranucleotide signature of the entire genome bin. This plot requires a file indicating the tetranucleotide signature of all sequences within the genome bins. This file can be creates with the tetra command.
• dist_plot: Produces a single figure combining the plots produced by gc_plot, coding_plot, and tetra_plot. This plot requires a file indicating the tetranucleotide signature of all sequences within the genome bins. This file can be creates with the tetra command.
• nx_plot: Produces a plot indicating the Nx value of a genome bin for all values of x. This provides a more comprehensive view of the quality of an assembly than simply considering N50.
• len_hist: Produce a histogram of the number of sequences within a genome bin at different sequence length intervals. This provides additional information regarding the quality of an assembled genome.
• marker_plot: Plots the position of marker genes on sequences within a genome bin. This provides information regarding the extent to which marker genes are collocated. The number of marker genes within a fixed size window (2.8 kbps in this example) is indicated by with different colours. Sequences without any marker genes are not shown.
• gc_bias_plot: