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Rashid U, Wu C, Shiller J, Smith K, Crowhurst R, Davy M, Chen TH, Carvajal I, Bailey S, Thomson S, Deng CH
Bioinformatics 40 (8) - [2024-08-02; online 2024-07-30]
Genome assembly projects have grown exponentially due to breakthroughs in sequencing technologies and assembly algorithms. Evaluating the quality of genome assemblies is critical to ensure the reliability of downstream analysis and interpretation. To fulfil this task, we have developed the AssemblyQC pipeline that performs file-format validation, contaminant checking, contiguity measurement, gene- and repeat-space completeness quantification, telomere inspection, taxonomic assignment, synteny alignment, scaffold examination through Hi-C contact-map visualization, and assessments of completeness, consensus quality and phasing through k-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualizations. The pipeline uses Nextflow for workflow orchestration and adheres to the best-practice established by the nf-core community. This pipeline offers a reproducible, scalable, and portable method to assess the quality of genome assemblies-the code is available online at GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc.
Bioinformatics Support and Infrastructure [Technology development]
Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed 39078114
DOI 10.1093/bioinformatics/btae477
Crossref 10.1093/bioinformatics/btae477
pii: 7723991
pmc: PMC11333564