Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases DOI Creative Commons
Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 23, 2023

Abstract Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, absence. In order properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able find not only reference sequences (previously identified in genomics database) that match their target taxa but also non-target taxa. Determining which have publicly available time-efficient accurate manner currently requires computational skills search, manipulate, parse multiple unconnected sequence databases. Our team iteratively designed Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) provides users efficient intuitive access genetic databases regardless of computer programming expertise. The returns number accessible barcode markers per organism NCBI Nucleotide, BOLD, CALeDNA CRUX Metabarcoding Databases. Depending on database, we offer various search filters such as min max length country origin. Users can then download FASTA/GenBank files from RSB web tool, view statistics about data, explore results determine details availability absence sequences.

Language: Английский

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data DOI Creative Commons
Katy E. Klymus, Jacoby Baker, Cathryn L. Abbott

et al.

Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8

Published: Dec. 30, 2024

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data metadata makes results difficult to reproduce synthesise. A working group scientists have collaborated produce set minimum reporting guidelines the constituent steps workflows, physical layout laboratories through archiving. We emphasise how suite should adhere findable, accessible, interoperable reproducible (FAIR) standards, thereby providing context evaluating understanding study results. An overview considerations each workflow step is presented then summarised in checklist that can accompany published or report. Ensuring workflows are transparent documented critical research allow more efficient uptake into management decision-making.

Language: Английский

Citations

2
A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species DOI Creative Commons
Jesús Zarcero, Adrià Antich, Marc Rius

et al.

iScience, Journal Year: 2023, Volume and Issue: 27(1), P. 108588 - 108588

Published: Nov. 25, 2023

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they often biased by inconsistent sampling methods incomplete reference databases. Logistic constraints prompt the development simple, easy-to-deploy samplers. We tested a new device called polyamide mesh organismal (POMPOM) with high surface-to-volume ratio. POMPOMS were deployed inside fishing recreational port Mediterranean alongside conventional settlement plates. also compiled curated database cytochrome oxidase (COI) sequences NIS. COI metabarcoding communities settled POMPOMs captured similar biodiversity than plates, shared molecular operational units (MOTUs) representing ca. 99% reads. 38 NIS detected accounting 26% easy to deploy handle provide an efficient method surveillance.

Language: Английский

Citations

5
Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases DOI Creative Commons
Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(10), P. e0309707 - e0309707

Published: Oct. 31, 2024

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, absence. In order properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able find not only reference sequences (previously identified in genomics database) that match their target taxa but also non-target taxa. Determining which have publicly available time-efficient accurate manner currently requires computational skills search, manipulate, parse multiple unconnected sequence databases. Our team iteratively designed Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) provides users efficient intuitive access genetic databases regardless of computer programming expertise. The returns number accessible barcode markers per organism NCBI Nucleotide, BOLD, CALeDNA CRUX Metabarcoding Databases. Depending on database, we offer various search filters such as min max length country origin. Users can then download FASTA/GenBank files from RSB web tool, view statistics about data, explore results determine details availability absence sequences.

Language: Английский

Citations

0
Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases DOI Creative Commons
Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 23, 2023

Abstract Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, absence. In order properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able find not only reference sequences (previously identified in genomics database) that match their target taxa but also non-target taxa. Determining which have publicly available time-efficient accurate manner currently requires computational skills search, manipulate, parse multiple unconnected sequence databases. Our team iteratively designed Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) provides users efficient intuitive access genetic databases regardless of computer programming expertise. The returns number accessible barcode markers per organism NCBI Nucleotide, BOLD, CALeDNA CRUX Metabarcoding Databases. Depending on database, we offer various search filters such as min max length country origin. Users can then download FASTA/GenBank files from RSB web tool, view statistics about data, explore results determine details availability absence sequences.

Language: Английский

Citations

0