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This is the development version of cogeqc; for the stable release version, see cogeqc.

Systematic quality checks on comparative genomics analyses

Bioconductor version: Development (3.20)

cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

Citation (from within R, enter citation("cogeqc")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Assessing genome assembly and annotation quality HTML R Script
Assessing orthogroup inference HTML R Script
Assessing synteny identification HTML R Script
Reference Manual PDF


biocViews ComparativeGenomics, FunctionalGenomics, GenomeAssembly, Network, Phylogenetics, QualityControl, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0)
Imports utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings
System Requirements BUSCO (>= 5.1.3)
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Suggests testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr
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Source Package cogeqc_1.9.0.tar.gz
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macOS Binary (x86_64) cogeqc_1.9.0.tgz
macOS Binary (arm64) cogeqc_1.9.0.tgz
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