nf-core/genomeqc

nf-core/genomeqc is an nf-core pipeline written in Nextflow designed to assess the quality of genome assemblies and their respective annotations using an ensuite of tools and custom scripts.

Overview

nf-core/genomeqc assessess the assembly quality based on:

• Contiguity:
  • Metrics such as the N50.
• Completeness:
  • Presence of telomeric repeats Benchmarking Universal Single-Copy Orthologs, and k-amers.
• Contamination:
  • Genome contamination screening.
  • Sequence clasiffication (Archaea, Bacteria, Prokarya, Eukaryota, organelles or unknown).
• Other:
  • Presence and number of Transposable Elements.
  • Gene stats (gene number, overlapping genes, mean gene length, etc.).

Additionally, the pipeline runs OrthoFinder for phylogenetic orthology inference and plots the results in an easy-to-visualize and comparable way.

For additional details, usage instructions, and examples, please refer to the nf-core/genomeqc GitHub repository.