ArticleInternational journal of molecular sciences2020
Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 41 citations in OpenAlex.
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- Comparative genomic analysis of metal-tolerant bacteria reveals significant differences in metal adaptation strategies.Microbiology spectrum · 2025Article
- Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.Respiratory research · 2025Article
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.G3 (Bethesda, Md.) · 2024Article
- Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.Environmental microbiome · 2024Article
- Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads.Microorganisms · 2024Article
- Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat,NAR genomics and bioinformatics · 2023Article
- Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data.Journal of fungi (Basel, Switzerland) · 2023Article
- De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing.Nucleic acids research · 2023Article
- Whole-genome sequencing and evolutionary analysis of the wild edible mushroom,Frontiers in microbiology · 2023Article
- Accuracy and Completeness of Long Read Metagenomic Assemblies.Microorganisms · 2022Article
- Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations.GigaScience · 2022Article
- A step forward for Shiga toxin-producingMicrobial genomics · 2022Article
- Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Plants (Basel, Switzerland) · 2022Article
- MAECI: A pipeline for generating consensus sequence with nanopore sequencing long-read assembly and error correction.PloS one · 2022Article
- Comparing Long-Read Assemblers to Explore the Potential of a Sustainable Low-Cost, Low-Infrastructure Approach to Sequence Antimicrobial Resistant Bacteria With Oxford Nanopore Sequencing.Frontiers in microbiology · 2022Article
- Comparison of De Novo Assembly Strategies for Bacterial Genomes.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.