ArticleNucleic acids research2023
Pest Alert Tool-a web-based application for flagging species of concern in metabarcoding datasets.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- BIOWATCH: a R shiny application for the detection of species of interest in metabarcoding datasets.BMC bioinformatics · 2026Article
- Aligning observation to action: Integrated monitoring for tropical seascape conservation and restoration.iScience · 2026Review
- Article
- Article
- A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species.iScience · 2024Article
- CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning.The CRISPR journal · 2023Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app-Pest Alert Tool-for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information's BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.
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Registered trials
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