acvill/binsummary.r

Combine data from CheckM, CheckM2, and GTDB-Tk

binSummary.R

Combine data from CheckM, CheckM2, and GTDB-Tk into a single report

Usage & Inputs

export PATH=/programs/R-4.2.0/bin:$PATH
Rscript binSummary.R \
    -q quality_report.tsv \
    -a abundance_report.tsv \
    -g gtdbtk.bac120.summary.tsv \
    -n sample \
    -o /path/to/outdir

Option	Description
-q / --quality_report	REQUIRED: completeness and contamination report generated by checkm2 predict
-a / --abundance_report	REQUIRED: abundance report generated by checkm profile
-g / --gtdbtk	REQUIRED: taxa report generated by gtdbtk classify_wf
-o / --out_dir	Output directory without trailing / (default: getwd())
-n / --name	REQUIRED: sample name to append to output file (${name}_binSummary.txt)

Output

The output file has 18 fields.

Field	Description
bin	bin name
contamination	checkm2 predict: percent contamination
model	checkm2 predict: completeness model
completeness	checkm2 predict: percent completeness
Mbp	bin size
mapped_reads	reads mapping to contigs comprising the bin
percent_mapped_reads	checkm profile: (reads mapped to bin)/(total number of reads mapped to assembly)
percent_binned_populations	checkm profile: the proportion of a bin relative to all recovered bins
percent_community	checkm profile: the proportion of a bin relative to the number of reads mapped to the assembly, adjusted for bin size
domain	from gtbtk classify_wf
phylum	...
class	...
order	...
family	...
genus	...
species	...
closest_reference	closest RefSeq predicted by gtbtk classify_wf
gtdbtk_warnings	notes from gtbtk classify_wf

Notes

• binSummary.R makes use of the native pipe and therefore requires R ≥ 4.1.0.
• the script will attempt to install optparse, dplyr, readr, tidyr, and stringr if not already installed
• tested with CheckM v1.2.1, CheckM2 v0.1.3, and GTDB-Tk v2.1.1