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Introduction

• About - What is CheckM?
• Citing - How can I cite CheckM?
• Contact Information - Who should I contact?
• Google Group - Post questions to the community!
• Contributors - People making CheckM better!

Bugs and Feature Requests

• Processing Large Numbers of Genomes - Process in batches!
• Bug Report - How can I report a bug?
• Feature Requests - How can I request a new feature?
• Known Issues - Are there any known issues?

Installation

The latest release of CheckM is v1.0.15 (August 8, 2019).

• System Requirements - What sort of computer is required to run CheckM?
• Installation - How can I install CheckM?
• Upgrade - How can I upgrade CheckM to the latest release?
• Unit Tests - How can I test my CheckM installation?
• KBase - CheckM is available online through KBase!

Quick Start

• Typical Workflow - What is the typical workflow for CheckM?
• Example Usage - How do I run CheckM?

Command Line Overview

• Overview - list of all CheckM features

Workflow Overview

• Lineage-specific Workflow - quality estimates with lineage-specific markers
• Taxonomic-specific Workflow - quality estimates with taxonomic-specific markers
• Using Custom Marker Genes - genome quality estimates with custom markers

Genome Quality Commands

• tree - place bins in the reference genome tree
• tree_qa - assess phylogenetic markers found in each bin
• lineage_set - infer lineage-specific marker sets for each bin
• taxon_list - list available taxonomic-specific marker sets
• taxon_set - infer taxonomic-specific marker set
• analyze - identify marker genes in bins
• qa - assess bins for contamination and completeness

Reported Statistics

• qa - description of statistics reported by qa command

Plots

• bin_qa_plot - bar plot of bin completeness, contamination, and strain heterogeneity
• gc_plot - create GC histogram and delta-GC plot
• coding_plot - create coding density (CD) histogram and delta-CD plot
• tetra_plot - create tetranucleotide distance (TD) histogram and delta-TD plot
• dist_plot - create image with GC, CD, and TD distribution plots together
• nx_plot - create Nx-plots
• len_plot - cumulative sequence length plot
• len_hist - sequence length histogram
• marker_plot - plot position of marker genes on sequences
• par_plot - parallel coordinate plot of GC and coverage
• gc_bias_plot - plot bin coverage as a function of GC
• cov_pca - PCA plot of coverage profiles
• tetra_pca - PCA plot of tetranucleotide signatures

Bin Exploration and Modification

• unique - ensure no sequences are assigned to multiple bins
• merge - identify bins with complementary sets of marker genes
• bin_compare - compare two sets of bins (e.g., from alternative binning methods)
• outliers - identify outliers in bins relative to reference distributions
• modify - modify sequences in a bin

Utility Commands

• unbinned - identify unbinned sequences
• coverage - calculate coverage of sequences
• tetra - calculate tetranucleotide signature of sequences
• profile - calculate percentage of reads mapped to each bin
• join_tables - join tab-separated value tables containing bin information
• ssu_finder - identify SSU (16S/18S) rRNAs in sequences