AssemblyQC: A NextFlow Pipeline for Reproducible Reporting of Assembly Quality

Usman Rashid; Chen Wu; Jason Shiller; Ken Smith; Ross Crowhurst; Marcus Davy; Ting-Hsuan Chen; Ignacio Carvajal; Sarah Bailey; Susan Thomson; Cecilia Deng

doi:10.20944/preprints202406.0518.v1

Preprint Technical Note Version 1 Preserved in Portico This version is not peer-reviewed

Version 1 : Received: 7 June 2024 / Approved: 7 June 2024 / Online: 10 June 2024 (06:39:41 CEST)

Summary 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 visualisation, and assessments of completeness, consensus quality and phasing through K-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualisations. Availability and Implementation 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.GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc Supplementary information Pipeline usage documentation, parameter descriptions and example outputs are available on GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc/tree/main/docs. A preview report is also hosted online: https://plant-food-research-open.github.io/assemblyqc

Genome; Quality assessment; Nextflow

Biology and Life Sciences, Other

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AssemblyQC: A NextFlow Pipeline for Reproducible Reporting of Assembly Quality

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