Metabarcoding protocol – Analysis of protists using the 18S rRNA gene and a DADA2 pipeline

Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

Vuorio, Kristiina
Mäki, Anita
Salmi, Pauliina
Aalto, Sanni L.
Tiirola, Marja

January 2020

The composition of phytoplankton community is the basis for environmental monitoring and assessment ...

Metabarcoding vs. morphological identification for aquatic ecosystem biomonitoring: a case study

Capelli, C.
Domaizon, I.
Eleršek T.
Kurmayer R.
Lepori, F
Dr Mischke
U. Rotta
Vautier, M.
Salmaso, N.

January 2021

Phytoplankton and benthic diatoms are frequently used as biological quality indicators. However, co...

Validation of a universal set of primers to study animal-associated microeukaryotic communities

Campo, Javier del
Pons, Maria J.
Herranz, Maria
Wakeman, Kevin C.
Valle, Juana del
Vermeij, Mark J.A.
Leander, Brian S.
Keeling, Patrick J.

October 2019

7 pages, 2 figures, supporting information https://doi.org/10.1111/1462-2920.14733The application of...

Metabarcoding protocol – Analysis of Bacteria (including Cyanobacteria) using the 16S rRNA gene and a DADA2 pipeline

Nico Salmaso
Giulia Riccioni
Massimo Pindo
Valentin Vasselon
Isabelle Domaizon
Rainer Kurmayer

August 2021

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) ...

metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes Dos Santos, Adriana

January 2022

In recent years, metabarcoding has become the method of choice for investigating the composition and...

metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana

January 2022

In recent years, metabarcoding has become the method of choice for investigating the composition and...

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Geisen, Stefan
Vaulot, Daniel
Mahe, Frederic
Lara, Enrique
de Vargas, Colomban
Bass, David

January 2019

Protists – all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonom...

metaPR 2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana

January 2022

International audienceProtists, that is, microbial eukaryotes that are not plants, animals or fungi ...

Biodiversity of Alpine ecosystems in a changing world (BIOALPEC): the focus on Alpine inland water ecosystems

Vettorazzo, S.
Boscaini, A.
Bruno, M. C.
Cerasino, L.
Obertegger, U.
Tolotti, M.
Salmaso, N.

January 2023

The “Biodiversity of Alpine ecosystems in a changing world” (BIOALPEC) project, carried out within t...

pr2-primers: An 18S rRNA primer database for protists

Vaulot, Daniel
Geisen, Stefan
Mahé, Frédéric
Bass, David

January 2021

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in...

Short- and long-read metabarcoding of the eukaryotic rRNA operon : Evaluation of primers and comparison to shotgun metagenomics sequencing

Latz, Meike A. C.
Grujcic, Vesna
Brugel, Sonia
Lycken, Jenny
John, Uwe
Karlson, Bengt
Andersson, Agneta
Andersson, Anders F.

January 2022

High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last de...

Metabarcoding and environmental sequencing projects

Kandaurova, Ekaterina

January 2023

The thesis explores the use of metabarcoding in projects uncovering biological diversity and its app...

Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses.

Cecchetto M.
Di Cesare A.
Eckert E.
Moro I.
Fontaneto D.
Schiaparelli S.

January 2022

The temporal dynamics of coastal planktic communities can be disclosed through DNA metabarcoding on ...

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

Djemiel, Christophe
Dequiedt, Samuel
Karimi, Battle
Cottin, Aurélien
Girier, Thibault
El Djoudi, Yassin
Wincker, Patrick
Mondy, Samuel
Chemidlin Prévost-Bouré, Nicolas
Maron, Pierre-Alain
Ranjard, Lionel
Terrat, Sébastien

February 2020

Background: The ability to compare samples or studies easily using metabarcoding so as to better in...

DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

Salmaso Nico
Vasselon Valentin
Rimet Frédéric
Vautier Marine
Elersek Tina
Boscaini Adriano
Donati Claudio
Moretto Marco
Pindo Massimo
Riccioni Giulia
Stefani Erika
Capelli Camilla
Lepori Fabio
Kurmayer Rainer
Mischke Ute
Krivograd Klemenčič Aleksandra
Novak Katarina
Greco Claudia
Franzini Giorgio
Fusato Giampaolo
Giacomazzi Federica
Lea Alessia
Menegon Silvia
Zampieri Chiara
Macor Arianna
Virgilio Damiano
Zanut Elisa
Zorza Raffaella
Buzzi Fabio
Domaizon Isabelle

April 2022

This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) -...

Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

Vuorio, Kristiina
Mäki, Anita
Salmi, Pauliina
Aalto, Sanni L.
Tiirola, Marja

January 2020

The composition of phytoplankton community is the basis for environmental monitoring and assessment ...

Metabarcoding vs. morphological identification for aquatic ecosystem biomonitoring: a case study

Capelli, C.
Domaizon, I.
Eleršek T.
Kurmayer R.
Lepori, F
Dr Mischke
U. Rotta
Vautier, M.
Salmaso, N.

January 2021

Phytoplankton and benthic diatoms are frequently used as biological quality indicators. However, co...

Validation of a universal set of primers to study animal-associated microeukaryotic communities

Campo, Javier del
Pons, Maria J.
Herranz, Maria
Wakeman, Kevin C.
Valle, Juana del
Vermeij, Mark J.A.
Leander, Brian S.
Keeling, Patrick J.

October 2019

7 pages, 2 figures, supporting information https://doi.org/10.1111/1462-2920.14733The application of...

Metabarcoding protocol – Analysis of Bacteria (including Cyanobacteria) using the 16S rRNA gene and a DADA2 pipeline

Nico Salmaso
Giulia Riccioni
Massimo Pindo
Valentin Vasselon
Isabelle Domaizon
Rainer Kurmayer

August 2021

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) ...

metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes Dos Santos, Adriana

January 2022

In recent years, metabarcoding has become the method of choice for investigating the composition and...

metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana

January 2022

In recent years, metabarcoding has become the method of choice for investigating the composition and...

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Geisen, Stefan
Vaulot, Daniel
Mahe, Frederic
Lara, Enrique
de Vargas, Colomban
Bass, David

January 2019

Protists – all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonom...

metaPR 2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana

January 2022

International audienceProtists, that is, microbial eukaryotes that are not plants, animals or fungi ...

Biodiversity of Alpine ecosystems in a changing world (BIOALPEC): the focus on Alpine inland water ecosystems

Vettorazzo, S.
Boscaini, A.
Bruno, M. C.
Cerasino, L.
Obertegger, U.
Tolotti, M.
Salmaso, N.

January 2023

The “Biodiversity of Alpine ecosystems in a changing world” (BIOALPEC) project, carried out within t...

pr2-primers: An 18S rRNA primer database for protists

Vaulot, Daniel
Geisen, Stefan
Mahé, Frédéric
Bass, David

January 2021

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in...

Short- and long-read metabarcoding of the eukaryotic rRNA operon : Evaluation of primers and comparison to shotgun metagenomics sequencing

Latz, Meike A. C.
Grujcic, Vesna
Brugel, Sonia
Lycken, Jenny
John, Uwe
Karlson, Bengt
Andersson, Agneta
Andersson, Anders F.

January 2022

High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last de...

Metabarcoding and environmental sequencing projects

Kandaurova, Ekaterina

January 2023

The thesis explores the use of metabarcoding in projects uncovering biological diversity and its app...

Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses.

Cecchetto M.
Di Cesare A.
Eckert E.
Moro I.
Fontaneto D.
Schiaparelli S.

January 2022

The temporal dynamics of coastal planktic communities can be disclosed through DNA metabarcoding on ...

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

Djemiel, Christophe
Dequiedt, Samuel
Karimi, Battle
Cottin, Aurélien
Girier, Thibault
El Djoudi, Yassin
Wincker, Patrick
Mondy, Samuel
Chemidlin Prévost-Bouré, Nicolas
Maron, Pierre-Alain
Ranjard, Lionel
Terrat, Sébastien

February 2020

Background: The ability to compare samples or studies easily using metabarcoding so as to better in...

DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

Salmaso Nico
Vasselon Valentin
Rimet Frédéric
Vautier Marine
Elersek Tina
Boscaini Adriano
Donati Claudio
Moretto Marco
Pindo Massimo
Riccioni Giulia
Stefani Erika
Capelli Camilla
Lepori Fabio
Kurmayer Rainer
Mischke Ute
Krivograd Klemenčič Aleksandra
Novak Katarina
Greco Claudia
Franzini Giorgio
Fusato Giampaolo
Giacomazzi Federica
Lea Alessia
Menegon Silvia
Zampieri Chiara
Macor Arianna
Virgilio Damiano
Zanut Elisa
Zorza Raffaella
Buzzi Fabio
Domaizon Isabelle

April 2022

This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) -...

Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

Vuorio, Kristiina
Mäki, Anita
Salmi, Pauliina
Aalto, Sanni L.
Tiirola, Marja

January 2020

The composition of phytoplankton community is the basis for environmental monitoring and assessment ...

Metabarcoding vs. morphological identification for aquatic ecosystem biomonitoring: a case study

Capelli, C.
Domaizon, I.
Eleršek T.
Kurmayer R.
Lepori, F
Dr Mischke
U. Rotta
Vautier, M.
Salmaso, N.

January 2021

Phytoplankton and benthic diatoms are frequently used as biological quality indicators. However, co...

Validation of a universal set of primers to study animal-associated microeukaryotic communities

Campo, Javier del
Pons, Maria J.
Herranz, Maria
Wakeman, Kevin C.
Valle, Juana del
Vermeij, Mark J.A.
Leander, Brian S.
Keeling, Patrick J.

October 2019

7 pages, 2 figures, supporting information https://doi.org/10.1111/1462-2920.14733The application of...

Metabarcoding protocol – Analysis of protists using the 18S rRNA gene and a DADA2 pipeline

Abstract

Extracted data

Metabarcoding protocol – Analysis of protists using the 18S rRNA gene and a DADA2 pipeline

Abstract

Extracted data

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