ArticleGenome biology2024
Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
- Article
- FuFiHLA: a tool for full-field HLA typing from long-read data.Bioinformatics (Oxford, England) · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
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Authors and funding
5 authors.
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Abstract
backgroundLong-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges.
resultsOur study evaluates recommended data types and volumes required to establish a robust de novo genome assembly pipeline for population-level pangenome projects, extensively examining performance between ONT's Duplex and PacBio HiFi datasets in the context of achieving high-quality phased genomes with enhanced contiguity and completeness. The results show that achieving chromosome-level haplotype-resolved assembly requires 20 × high-quality long reads such as PacBio HiFi or ONT Duplex, combined with 15-20 × of ultra-long ONT per haplotype and 10 × of long-range data such as Omni-C or Hi-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in phasing accuracies, while Duplex generates more T2T contigs.
conclusionOur study provides insights into optimal data types and volumes for robust de novo genome assembly in population-level pangenome projects. Reassessing the recommended data types and volumes in this study and aligning them with practical economic limitations are vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.
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