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. 2024 Aug 2;40(8):btae477.
doi: 10.1093/bioinformatics/btae477.

AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality

Usman Rashid  1 , Chen Wu  1 , Jason Shiller  2 , Ken Smith  1 , Ross Crowhurst  1 , Marcus Davy  2 , Ting-Hsuan Chen  3 , Ignacio Carvajal  1 , Sarah Bailey  1 , Susan Thomson  3 , Cecilia H Deng  1
Affiliations

AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality

Usman Rashid et al. Bioinformatics. .

Abstract

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 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.

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 at GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Pipeline flowchart.
See this image and copyright information in PMC

References

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Publication types

Grants and funding