ArticlePeerJ2019
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.Molecular ecology resources · 2025Article
- A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.eLife · 2024Article
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge.BMC genomics · 2022Article
- Article
- Article
- On the optimistic performance evaluation of newly introduced bioinformatic methods.Genome biology · 2021Article
- Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences.Frontiers in microbiology · 2021Article
- HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.Frontiers in microbiology · 2021Article
- A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses.Ecology and evolution · 2020Article
- Metagenomics as a Tool To Monitor Reclaimed-Water Quality.Applied and environmental microbiology · 2020Review
- LEMMI: a continuous benchmarking platform for metagenomics classifiers.Genome research · 2020Article
- Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella.American journal of botany · 2020Article
- TAMA: improved metagenomic sequence classification through meta-analysis.BMC bioinformatics · 2020Article
- Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.Frontiers in microbiology · 2020Article
- Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance.GigaScience · 2019Review
- Essential guidelines for computational method benchmarking.Genome biology · 2019Review
- A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction forFrontiers in microbiology · 2019Article
- Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.Environmental DNA (Hoboken, N.J.)Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust
Indexed as
Identifiers
What OpenQuestion holds
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.