AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.
Bioinformatics
; 40(8)2024 08 02.
Article
en En
| MEDLINE
| ID: mdl-39078114
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.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2024
Tipo del documento:
Article
País de afiliación:
Nueva Zelanda
Pais de publicación:
Reino Unido