nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality

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Abstract The rapid growth in publicly available genome assemblies has made selecting genomes suitable for downstream analyses increasingly challenging. Differences in assembly and annotation quality can influence gene completeness, duplication rates, contiguity, repeat representation, and other characteristics. Assessing genome quality therefore requires integrating multiple complementary quality metrics that are often generated by independent tools. Here, we present nf-core/genomeqc , a workflow for assessing and comparing genome assemblies. The pipeline accepts RefSeq/GenBank accessions for automatic genome and annotation retrieval, or local genome (FASTA) and annotation (GFF3/GTF) files. It integrates complementary analyses of assembly contiguity, gene completeness, annotation quality, repeat content and other quality metrics using tools such as BUSCO, QUAST, Merqury, and AGAT, before combining the results on a phylogenetic tree for visualisation and comparison across species. GenomeQC is implemented in Nextflow within the nf-core framework, providing an accessible, reproducible, scalable and community-driven workflow for genome quality assessment.

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