Code and data for “Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package”

Preface

This book contains all code and data used in the paper Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package, and it is intended to make all analyses fully reproducible.

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ABSTRACT

Comparative genomics has become an indispensable part of modern biology due to the advancements in high-throughput sequencing technologies and the accumulation of genomic data in public databases. However, the quality of genomic data and the choice of parameters used in software tools used for comparative genomics can greatly impact the accuracy of results. To address these issues, we present cogeqc, an R/Bioconductor package that provides researchers with a toolkit to assess genome assembly and annotation quality, orthogroup inference, and synteny detection. The package offers context-guided assessments of assembly and annotation statistics by comparing observed statistics to those of closely-related species on NCBI. To assess orthogroup inference, cogeqc calculates a protein domain-aware orthogroup score that aims at maximizing the number of shared protein domains within the same orthogroup. The assessment of synteny detection consists in representing anchor gene pairs as a synteny network and analyzing its graph properties, such as clustering coefficient, node count, and scale-free topology fit. The application of cogeqc to real data sets allowed for an evaluation of multiple parameter combinations for orthogroup inference and synteny detection, providing researchers with guidelines to aid in the selection of the most appropriate tools and parameters for their specific data.