ArticleBriefings in bioinformatics2019
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.
Article in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Telomere-to-Telomere Genome Assembly of TwoBiomolecules · 2026Article
- Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness.Scientific reports · 2025Article
- Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.Bioinformatics (Oxford, England) · 2025Article
- Comparative Analysis of Virulence Genes in Non-Tuberculosis Mycobacteria (NTM) Isolated from Kenyan Camel Milk Suggests Potential Pathogenicity.Current microbiology · 2025Article
- Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.Microorganisms · 2025Review
- GoldPolish-target: targeted long-read genome assembly polishing.BMC bioinformatics · 2025Article
- xRead: a coverage-guided approach for scalable construction of read overlapping graph.GigaScience · 2025Article
- Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.Molecular ecology resources · 2025Article
- Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcriptome analysis of nitrogen assimilation preferences inFrontiers in microbiology · 2025Article
- Chromosome-level genome assembly of the Suminoe oyster Crassostrea ariakensis in south China.Scientific data · 2024Article
- Biosynthetic gene clusters with biotechnological applications in novel Antarctic isolates from Actinomycetota.Applied microbiology and biotechnology · 2024Article
- NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.Genome biology · 2024Article
- High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Unraveling the dynamic transcriptomic changes during the dimorphic transition ofFrontiers in microbiology · 2024Article
- A practical assembly guideline for genomes with various levels of heterozygosity.Briefings in bioinformatics · 2023Article
- De novo full length transcriptome analysis of a naturally caffeine-free tea plant reveals specificity in secondary metabolic regulation.Scientific reports · 2023Article
- Transcript- and annotation-guided genome assembly of the European starling.Molecular ecology resources · 2022Article
- Decrypting the complexity of the human malaria parasite biology through systems biology approaches.Frontiers in systems biology · 2022Article
Corrections and comments
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.
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