nf-core/reportho: a pipeline for comparative analysis of ortholog predictions

Orthology is a highly relevant aspect of genomics, as orthologous genes allow functional inference, identify certain evolutionary constraints and are used for reconstructing the tree of life. This is especially important in light of new massive sequencing initiatives, most importantly the Earth Biogenome Project. There is a large variety of publicly available orthology prediction methods, but the results they provide are highly varied and agreement is limited. Significant effort is made to assess the performance of those methods, most notably through the ongoing Quest for Orthologs, which created a comprehensive benchmark for orthology prediction. We propose nf-core/reportho, a Nextflow pipeline for comparative analysis of ortholog predictions. The pipeline analyzes the predictions from the perspective of a single query protein. The pipeline retrieves orthology predictions from public sources, performs comparative analysis, calculates agreement statistics and creates multiple visual representations. It also provides basic downstream analysis in the form of MSA and phylogenetic reconstruction. We envision that nf-core/reportho will enable and accelerate new research projects involving specific proteins, as well as systematic investigation of orthology databases.