ArticleBMC bioinformatics2020
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review.Parasites & vectors · 2024Pooled it
- Integrative genomic and phenotypic analyses reveal broad-spectrum antifungal activity and biocontrol potential in Bacillus ayatagriensis.Functional & integrative genomics · 2026Article
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Primer-Less Species Identification Throughout Fungal (International journal of molecular sciences · 2026Article
- Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.BMC microbiology · 2026Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.NPJ biofilms and microbiomes · 2025Article
- Real-time analysis and visualization of nanopore metagenomic samples with MARTi.Genome research · 2025Article
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Automated environmental metagenomics using Oxford nanopore sequencing.BMC genomics · 2025Article
- Physiological changes and full-length transcriptome of Artemisia sphaerocephala in response to drought stress.BMC plant biology · 2025Article
- Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.Microbial ecology · 2025Article
- Significant variations of bacterial communities among the developmental stages of Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae).Scientific reports · 2025Article
- Beyond Low Prevalence: Exploring Antibiotic Resistance and Virulence Profiles in Sri Lankan Helicobacter pylori with Comparative Genomics.Microorganisms · 2025Article
- Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.Frontiers in microbiology · 2025Article
- Causal links between obesity, lipids, adipokines, and cognition: a bidirectional Mendelian-randomization analysis.Frontiers in endocrinology · 2025Article
- The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.PeerJ · 2025Article
- Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis.Experimental hematology · 2024Review
- Using nanopore sequencing to identify bacterial infection in joint replacements: a preliminary study.Briefings in functional genomics · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities.
resultsHere we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus). We then show that for two popular taxonomic classifiers, long reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities.
conclusionsThis work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.
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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.