AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

Autor:	Rashid U; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Wu C; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Shiller J; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 3182 Te Puke, New Zealand., Smith K; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Crowhurst R; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Davy M; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 3182 Te Puke, New Zealand., Chen TH; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 7608 Lincoln, New Zealand., Carvajal I; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Bailey S; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand., Thomson S; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 7608 Lincoln, New Zealand., Deng CH; Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Aug 02; Vol. 40 (8).
DOI:	10.1093/bioinformatics/btae477
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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