ArticleGenome research2024
Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Time-Efficient and Informatic-Skill-Light Gap-Filling for Telomere-to-Telomere Genome Assembly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- T2TJournal of fungi (Basel, Switzerland) · 2026Article
- Chromosome-scale genome assembly of Flemingia macrophylla.Scientific data · 2025Article
- RAGA: a reference-assisted genome assembly tool for efficient population-scale assembly.Horticulture research · 2025Article
- Precision medicine in liver transplantation for hepatocellular carcinoma: applications and prospects of third-generation sequencing technology.Journal of cancer research and clinical oncology · 2025Review
- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- A near telomere-to-telomere phased reference assembly for the male mountain gorilla.Scientific data · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing.International journal of molecular sciences · 2025Review
- Chromosome-level genome assembly of an endoparasitoid Cotesia ruficrus.Scientific data · 2025Article
- Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.International journal of molecular sciences · 2024Review
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- DecipheringFrontiers in immunology · 2024Article
- Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.
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