diff --git a/api/modules.json b/api/modules.json index 10c13c01..efc1ec50 100644 --- a/api/modules.json +++ b/api/modules.json @@ -22,7 +22,7 @@ "video": "assembly/largegenome/tutorial" }, { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" } ] }, @@ -177,10 +177,10 @@ "title": "Friday: Microbiome", "trainings": [ { - "session": "metagenomics/mothur-miseq-sop-short" + "session": "microbiome/mothur-miseq-sop-short" }, { - "session": "metagenomics/nanopore" + "session": "microbiome/nanopore" } ] } @@ -863,13 +863,13 @@ "title": "Taxonomic Profiling", "trainings": [ { - "video": "metagenomics/introduction/slides" + "video": "microbiome/introduction/slides" }, { - "video": "metagenomics/mothur-miseq-sop-short/tutorial" + "video": "microbiome/mothur-miseq-sop-short/tutorial" }, { - "video": "metagenomics/taxonomic-profiling/tutorial" + "video": "microbiome/taxonomic-profiling/tutorial" } ] }, @@ -877,7 +877,7 @@ "title": "Assembly", "trainings": [ { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" } ] }, @@ -885,19 +885,19 @@ "title": "Long-read microbiome sequencing", "trainings": [ { - "video": "metagenomics/pathogen-detection-from-nanopore-foodborne-data/tutorial" + "video": "microbiome/pathogen-detection-from-nanopore-foodborne-data/tutorial" }, { - "video": "metagenomics/beer-data-analysis/tutorial" + "video": "microbiome/beer-data-analysis/tutorial" }, { "video": "wetlab/miseq/demo" }, { - "video": "metagenomics/clinical-applications" + "video": "microbiome/clinical-applications" }, { - "video": "metagenomics/plasmid-metagenomics-nanopore/tutorial" + "video": "microbiome/plasmid-metagenomics-nanopore/tutorial" } ] }, @@ -905,7 +905,7 @@ "title": "Transcriptomics & Proteomics", "trainings": [ { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" }, { "video": "proteomics/metaproteomics/tutorial" @@ -923,13 +923,13 @@ "title": "Taxonomic Profiling", "trainings": [ { - "video": "metagenomics/introduction/slides" + "video": "microbiome/introduction/slides" }, { - "video": "metagenomics/mothur-miseq-sop-short/tutorial" + "video": "microbiome/mothur-miseq-sop-short/tutorial" }, { - "video": "metagenomics/taxonomic-profiling/tutorial" + "video": "microbiome/taxonomic-profiling/tutorial" } ] }, @@ -940,16 +940,16 @@ "video": "wetlab/miseq/demo" }, { - "video": "metagenomics/clinical-applications" + "video": "microbiome/clinical-applications" }, { - "video": "metagenomics/plasmid-metagenomics-nanopore/tutorial" + "video": "microbiome/plasmid-metagenomics-nanopore/tutorial" }, { - "video": "metagenomics/pathogen-detection-from-nanopore-foodborne-data/tutorial" + "video": "microbiome/pathogen-detection-from-nanopore-foodborne-data/tutorial" }, { - "video": "metagenomics/beer-data-analysis/tutorial" + "video": "microbiome/beer-data-analysis/tutorial" } ] }, @@ -957,13 +957,13 @@ "title": "Other", "trainings": [ { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" }, { "session": "variant-analysis/tb-variant-analysis" }, { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" }, { "video": "proteomics/metaproteomics/tutorial" @@ -1612,7 +1612,7 @@ "title": "Other trancriptomics tutorials", "trainings": [ { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" } ] } diff --git a/api/modules/assembly.json b/api/modules/assembly.json index b214bc0e..6710d8f5 100644 --- a/api/modules/assembly.json +++ b/api/modules/assembly.json @@ -21,7 +21,7 @@ "video": "assembly/largegenome/tutorial" }, { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" } ] }, diff --git a/api/modules/bioinformatics-buffet.json b/api/modules/bioinformatics-buffet.json index 020eaf9e..86ce02eb 100644 --- a/api/modules/bioinformatics-buffet.json +++ b/api/modules/bioinformatics-buffet.json @@ -66,10 +66,10 @@ "title": "Friday: Microbiome", "trainings": [ { - "session": "metagenomics/mothur-miseq-sop-short" + "session": "microbiome/mothur-miseq-sop-short" }, { - "session": "metagenomics/nanopore" + "session": "microbiome/nanopore" } ] } diff --git a/api/modules/meta-omics.json b/api/modules/meta-omics.json index bba3d86f..751694eb 100644 --- a/api/modules/meta-omics.json +++ b/api/modules/meta-omics.json @@ -7,13 +7,13 @@ "title": "Taxonomic Profiling", "trainings": [ { - "video": "metagenomics/introduction/slides" + "video": "microbiome/introduction/slides" }, { - "video": "metagenomics/mothur-miseq-sop-short/tutorial" + "video": "microbiome/mothur-miseq-sop-short/tutorial" }, { - "video": "metagenomics/taxonomic-profiling/tutorial" + "video": "microbiome/taxonomic-profiling/tutorial" } ] }, @@ -21,7 +21,7 @@ "title": "Assembly", "trainings": [ { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" } ] }, @@ -29,19 +29,19 @@ "title": "Long-read microbiome sequencing", "trainings": [ { - "video": "metagenomics/pathogen-detection-from-nanopore-foodborne-data/tutorial" + "video": "microbiome/pathogen-detection-from-nanopore-foodborne-data/tutorial" }, { - "video": "metagenomics/beer-data-analysis/tutorial" + "video": "microbiome/beer-data-analysis/tutorial" }, { "video": "wetlab/miseq/demo" }, { - "video": "metagenomics/clinical-applications" + "video": "microbiome/clinical-applications" }, { - "video": "metagenomics/plasmid-metagenomics-nanopore/tutorial" + "video": "microbiome/plasmid-metagenomics-nanopore/tutorial" } ] }, @@ -49,7 +49,7 @@ "title": "Transcriptomics & Proteomics", "trainings": [ { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" }, { "video": "proteomics/metaproteomics/tutorial" diff --git a/api/modules/microbial.json b/api/modules/microbial.json index bab1edbd..0c94dbca 100644 --- a/api/modules/microbial.json +++ b/api/modules/microbial.json @@ -6,13 +6,13 @@ "title": "Taxonomic Profiling", "trainings": [ { - "video": "metagenomics/introduction/slides" + "video": "microbiome/introduction/slides" }, { - "video": "metagenomics/mothur-miseq-sop-short/tutorial" + "video": "microbiome/mothur-miseq-sop-short/tutorial" }, { - "video": "metagenomics/taxonomic-profiling/tutorial" + "video": "microbiome/taxonomic-profiling/tutorial" } ] }, @@ -23,16 +23,16 @@ "video": "wetlab/miseq/demo" }, { - "video": "metagenomics/clinical-applications" + "video": "microbiome/clinical-applications" }, { - "video": "metagenomics/plasmid-metagenomics-nanopore/tutorial" + "video": "microbiome/plasmid-metagenomics-nanopore/tutorial" }, { - "video": "metagenomics/pathogen-detection-from-nanopore-foodborne-data/tutorial" + "video": "microbiome/pathogen-detection-from-nanopore-foodborne-data/tutorial" }, { - "video": "metagenomics/beer-data-analysis/tutorial" + "video": "microbiome/beer-data-analysis/tutorial" } ] }, @@ -40,13 +40,13 @@ "title": "Other", "trainings": [ { - "video": "metagenomics/metagenomics-assembly/tutorial" + "video": "microbiome/metagenomics-assembly/tutorial" }, { "session": "variant-analysis/tb-variant-analysis" }, { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" }, { "video": "proteomics/metaproteomics/tutorial" diff --git a/api/modules/transcriptomics.json b/api/modules/transcriptomics.json index 2959a1e4..52d14ff8 100644 --- a/api/modules/transcriptomics.json +++ b/api/modules/transcriptomics.json @@ -45,7 +45,7 @@ "title": "Other trancriptomics tutorials", "trainings": [ { - "video": "metagenomics/metatranscriptomics" + "video": "microbiome/metatranscriptomics" } ] } diff --git a/api/sessions.json b/api/sessions.json index fb473102..7bd43de4 100644 --- a/api/sessions.json +++ b/api/sessions.json @@ -123,6 +123,23 @@ "proteomics/proteogenomics-novel-peptide-analysis/tutorial" ] }, + "microbiome/mothur-miseq-sop-short": { + "title": "16S taxonomic profiling", + "description": "To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene\nis often used. This allows us to identify the bacterial species present in our sample.\nThis lecture and practical session introduces you to 16S analysis in Galaxy using the\nmothur tool suite.\n", + "videos": [ + "microbiome/introduction/slides", + "microbiome/mothur-miseq-sop-short/tutorial" + ] + }, + "microbiome/nanopore": { + "title": "Microbiome Analysis using Nanopore Sequencing", + "description": "In this 3-part module, you will learn about Nanopore long-read sequencing for the\ndetection of antimicrobial resistance (AMR). There is a short video showing you the\nwetlab steps involved in using the MinION sequencer. A talk about the clinical applications,\nand finally a practical tutorial walking you through an AMR analysis in Galaxy.\n", + "videos": [ + "wetlab/miseq/demo", + "microbiome/clinical-applications", + "microbiome/plasmid-metagenomics-nanopore/tutorial" + ] + }, "statistics/deeplearning": { "title": "Deep Learning Demystified", "description": "This 3-part session will introduce you to the world of deep learning and cover Feedforward\nNeural Networks (FNN), Recurrent Neural Networks (FNN), and Convolutional Neural Networks\n(CNN).\n", diff --git a/events.html b/events.html index 26ec56bf..9b9edbf3 100644 --- a/events.html +++ b/events.html @@ -2058,6 +2058,10 @@ + + + + diff --git a/modules/assembly.html b/modules/assembly.html index 88882dbd..380612d8 100644 --- a/modules/assembly.html +++ b/modules/assembly.html @@ -968,7 +968,7 @@

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Description:

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. +To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. +For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study +(six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.

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Length:1 hour
Captions: Bérénice Batut, Sophia Hampe
Created:2 May 2023
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Friday: Microbiome

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Friday: Microbiome

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To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene +is often used. This allows us to identify the bacterial species present in our sample. +This lecture and practical session introduces you to 16S analysis in Galaxy using the +mothur tool suite. +

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Introduction to Microbiome Analysis (Lecture)

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Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

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Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
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16S Microbial Analysis with mothur (short) (Tutorial)

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Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:1 hour 37 minutes
Captions: Saskia Hiltemann
Created:19 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
    • + +
  • Using a mock community to assess the error rate of your sequencing experiment
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  • Visualize sample diversity using Krona and Phinch
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In this 3-part module, you will learn about Nanopore long-read sequencing for the +detection of antimicrobial resistance (AMR). There is a short video showing you the +wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, +and finally a practical tutorial walking you through an AMR analysis in Galaxy. +

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This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

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Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
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Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

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Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

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Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
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Antibiotic resistance detection (Tutorial)

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This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
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  • Determine the structure of the genome(s)
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  • Scan for antimicrobial resistance genes with Staramr
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Taxonomic Profiling

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Taxonomic Profiling

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This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

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Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
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Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:1 hour 37 minutes
Captions: Saskia Hiltemann
Created:19 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
    • + +
  • Using a mock community to assess the error rate of your sequencing experiment
    • + +
  • Visualize sample diversity using Krona and Phinch
    • + +
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Length:1 hour 15 minutes
Captions: Sophia Hampe
Created:16 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + +
Learning Objectives: +
    + +
  • Explain what taxonomic assignment is
    • + +
  • Explain how taxonomic assignment works
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  • Apply Kraken and MetaPhlAn to assign taxonomic labels
    • + +
  • Apply Krona and Pavian to visualize results of assignment and understand the output
    • + +
  • Identify taxonomic classification tool that fits best depending on their data
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Description:

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. +To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. +For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study +(six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.

+
Length:1 hour
Captions: Bérénice Batut, Sophia Hampe
Created:2 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Describe what an assembly is
    • + +
  • Describe what de-replication is
    • + +
  • Explain the difference between co-assembly and individual assembly
    • + +
  • Explain the difference between reads, contigs and scaffolds
    • + +
  • Explain how tools based on De Bruijn graph work
    • + +
  • Apply appropriate tools for analyzing the quality of metagenomic data
    • + +
  • Construct and apply simple assembly pipelines on short read data
    • + +
  • Apply appropriate tools for analyzing the quality of metagenomic assembly
    • + +
  • Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome
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Long-read microbiome sequencing

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Description:

In this tutorial, we will be presenting a series of Galaxy workflows whose main goals are +1) to agnostically detect pathogens (What exactly is this pathogen and what virulence +factors does it carry?) from data extracted directly (without prior cultivation) from a +potentially contaminated sample (e.g. food like chicken, beef, etc.) and sequenced using +Nanopore, and 2) to compare different samples to trace the possible source of contamination

+
Length:1 hour 45 minutes
Captions: Engy Nasr
Created:1 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + +
Learning Objectives: +
    + +
  • Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
    • + +
  • Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
    • + +
  • Perform taxonomy profiling indicating and visualizing up to species level in the samples
    • + +
  • Identify pathogens based on the found virulence factor gene products via assembly, identify strains and indicate all antimicrobial resistance genes in samples
    • + +
  • Identify pathogens via SNP calling and build the consensus gemone of the samples
    • + +
  • Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + @@ -586,116 +1538,237 @@

Self Study Tutorial

-
+ + + + + + + + + + + + + + + +
+
+ +
+ +
+ +
+ + + + + + + + + + + + + + + + + + +
+
+

Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Length:1 hour 5 minutes
Captions: Sophia Hampe
Created:10 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + +
Learning Objectives: +
    + +
  • Inspect metagenomics data
    • + +
  • Run metagenomics tools
    • + +
  • Identify yeast species contained in a sequenced beer sample using DNA
    • + +
  • Visualize the microbiome community of a beer sample
    • + +
+
+ +
+ Go to the video page to see all versions. -

Assembly

- -

-

-
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+ + + -
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Speaker

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Self Study Tutorial

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- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - - - -
-

Instructor

- @@ -707,32 +1780,41 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
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Self Study Tutorial

-
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Long-read microbiome sequencing

- -

-

-
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Long-read microbi
-
-
-
+
- - - + + + -
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-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - -
-

Instructor

- + -
- - +
+
+

Demo Video

+
+
+
+ + + + + + + + + + + + -
- -
- - - - - - - - -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
-
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
- - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
+ + + + Captions: + Saskia Hiltemann + + + + + Created: + 15 February 2021 + + + + + + + Support: + +
+ + + + + + + + - - - +
+ + Go to the video page to see all versions. + +
+ + + -
-

Instructor

- +
+

Speaker

+ @@ -1034,32 +1977,37 @@

Self Study Tutorial

- -
+
+ + +
+ -
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Self Study Tutorial

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Self Study Tutorial

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Self Study Tutorial

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Demo Video

+

Lecture Video

+
+
+ + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + Known Working + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
-
- -
-
+ + Go to the video page to see all versions. + +
+ + + -
- -
- - - - - - - - -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - - - -
-

Instructor

- +
+

Speaker

+ @@ -1543,32 +2488,37 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
-
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Transcriptomics & Prot
@@ -1633,74 +2583,217 @@

Transcriptomics & Prot - - + + + + + + + + + + + +
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
+
+

Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.

+
Length:1 hour 5 minutes
Captions: Paul Zierep
Created:17 May 2023
Materials: + +
Support: + +
Supported Servers: + + - - - + + Known Working + + -
-

Instructor

- + + Possibly Working + + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ @@ -1712,32 +2805,37 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
-

diff --git a/modules/microbial.html b/modules/microbial.html index 1652f84d..3f7e98e5 100644 --- a/modules/microbial.html +++ b/modules/microbial.html @@ -132,7 +132,7 @@

Taxonomic Profiling

@@ -143,232 +143,143 @@

Taxonomic Profiling

- - - + + + -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - -
-

Instructor

- + -
- - +
+
+

Lecture Video

+
+
+
+ + + + + + + + + + + + -
- -
- - - - - - + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
Support: + +
Learning Objectives: +
    + +
+
- - - +
+ + Go to the video page to see all versions. + +
+ + + -
-

Instructor

- +
+

Speaker

+ @@ -380,32 +291,41 @@

Self Study Tutorial

- -
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+ + +
+ -
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-
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Self Study Tutorial

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Self Study Tutorial

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- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - -
-

Instructor

- + -
- - +
+
+

Tutorial Video

+
+ +
+
+ + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Length:1 hour 15 minutes
Captions: Sophia Hampe
Created:16 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + Known Working + + + +
Learning Objectives: +
    + +
  • Explain what taxonomic assignment is
    • + +
  • Explain how taxonomic assignment works
    • + +
  • Apply Kraken and MetaPhlAn to assign taxonomic labels
    • + +
  • Apply Krona and Pavian to visualize results of assignment and understand the output
    • + +
  • Identify taxonomic classification tool that fits best depending on their data
    • + +
+
- +
- - - - - - - - - - - - - - - - -
+ Go to the video page to see all versions. -
- -
- -
- -
- - - - - - - - -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - - +
+ + + -
-

Instructor

- +
+

Speaker

+ @@ -1058,32 +888,41 @@

Self Study Tutorial

- -
+
+ + +
+ -
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-
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Self Study Tutorial

+
+ + + + +

Microbiome Analysis using Nanopore Sequencing

+ +

+

+
+ @@ -1122,89 +972,1220 @@

Self Study Tutorial

-
- -
- +
+ +
+ +
+ +
+ +
+ + + + + + + + + + + + + + + + + + +
+
+

Demo Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + +
+
+
+ + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + + + + + + + + + + + + + + + + +
+
+

Lecture Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

+
Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + +
+
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+ + + + + + + + + + + + + + + + + + + + + + +
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+ +
+ +
+ + + + + + + + + + + + + + + + + + +
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Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + +
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Video

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

In this tutorial, we will be presenting a series of Galaxy workflows whose main goals are +1) to agnostically detect pathogens (What exactly is this pathogen and what virulence +factors does it carry?) from data extracted directly (without prior cultivation) from a +potentially contaminated sample (e.g. food like chicken, beef, etc.) and sequenced using +Nanopore, and 2) to compare different samples to trace the possible source of contamination

+
Length:1 hour 45 minutes
Captions: Engy Nasr
Created:1 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + +
Learning Objectives: +
    + +
  • Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
    • + +
  • Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
    • + +
  • Perform taxonomy profiling indicating and visualizing up to species level in the samples
    • + +
  • Identify pathogens based on the found virulence factor gene products via assembly, identify strains and indicate all antimicrobial resistance genes in samples
    • + +
  • Identify pathogens via SNP calling and build the consensus gemone of the samples
    • + +
  • Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + +
+
+
+ + + + + + + + + + + + + + + + + + + + + + +
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+ +
+ +
+ +
+ + + + + + + + + + + + + + + + + + +
+
+

Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Length:1 hour 5 minutes
Captions: Sophia Hampe
Created:10 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + +
Learning Objectives: +
    + +
  • Inspect metagenomics data
    • + +
  • Run metagenomics tools
    • + +
  • Identify yeast species contained in a sequenced beer sample using DNA
    • + +
  • Visualize the microbiome community of a beer sample
    • + +
+
+
+ + Go to the video page to see all versions. + +
+ + + -
- -
- - - - - - - - -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - - - -
-

Instructor

- +
+

Speaker

+ @@ -1216,32 +2197,41 @@

Self Study Tutorial

- -
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+ -
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Self Study Tutorial

+
+ + + + +

Other

+ +

+

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+ @@ -1282,256 +2283,196 @@

Self Study Tutorial

-
-
-
+
- - - + + + -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - -
-

Instructor

- + -
- - +
+
+

Video

+
+
+
+ + + + + + + + + + + + - - - -

Other

- -

-

-
- - - - - - - - - - + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. +To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. +For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study +(six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.

+
Length:1 hour
Captions: Bérénice Batut, Sophia Hampe
Created:2 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Describe what an assembly is
    • + +
  • Describe what de-replication is
    • + +
  • Explain the difference between co-assembly and individual assembly
    • + +
  • Explain the difference between reads, contigs and scaffolds
    • + +
  • Explain how tools based on De Bruijn graph work
    • + +
  • Apply appropriate tools for analyzing the quality of metagenomic data
    • + +
  • Construct and apply simple assembly pipelines on short read data
    • + +
  • Apply appropriate tools for analyzing the quality of metagenomic assembly
    • + +
  • Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome
    • + +
+
-
- -
-
+ + Go to the video page to see all versions. + +
+ + + -
- -
- - - - - - - - -
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
- - Go to the video page to see all versions. - -
- - - - - -
-

Instructor

- +
+

Speaker

+ @@ -1543,32 +2484,41 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
-
@@ -2048,7 +2998,7 @@

M. tuberculosis Variant Analysis (Tutorial)

@@ -2059,74 +3009,217 @@

M. tuberculosis Variant Analysis (Tutorial)

- - + + + + + + + + + + + +
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
+
+

Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.

+
Length:1 hour 5 minutes
Captions: Paul Zierep
Created:17 May 2023
Materials: + +
Support: + +
Supported Servers: + + - - - + + Known Working + + -
-

Instructor

- + + Possibly Working + + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ @@ -2138,32 +3231,37 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
-
diff --git a/modules/transcriptomics.html b/modules/transcriptomics.html index 70a2fc6f..40793532 100644 --- a/modules/transcriptomics.html +++ b/modules/transcriptomics.html @@ -2706,7 +2706,7 @@

Other trancriptomi
@@ -2717,74 +2717,217 @@

Other trancriptomi - - + + + + + + + + + + + +
-
-

Self Study Tutorial

-
- - image indicating this is a self-study session. - - This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions! -
-
- - - - - - - - - - - - - - - - - - - - - - - -
Tutorial:
Material: - - - GTN Tutorial - -
Support: - -
-
+
+

Tutorial Video

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.

+
Length:1 hour 5 minutes
Captions: Paul Zierep
Created:17 May 2023
Materials: + +
Support: + +
Supported Servers: + + - - - + + Known Working + + -
-

Instructor

- + + Possibly Working + + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ @@ -2796,32 +2939,37 @@

Self Study Tutorial

- -
+
+ + +
+ -
-
-

diff --git a/session-library.html b/session-library.html index 33dff99d..37fdf6ec 100644 --- a/session-library.html +++ b/session-library.html @@ -8839,6 +8839,2728 @@

Proteogenomics 3: Novel peptide analysis (Demo) Metagenomics

+ + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + +

To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene +is often used. This allows us to identify the bacterial species present in our sample. +This lecture and practical session introduces you to 16S analysis in Galaxy using the +mothur tool suite. +

+ + + + + + + + + + + + + + + + + + +
+
+

Introduction to Microbiome Analysis (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
Support: + +
Learning Objectives: +
    + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

16S Microbial Analysis with mothur (short) (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:1 hour 37 minutes
Captions: Saskia Hiltemann
Created:19 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
    • + +
  • Using a mock community to assess the error rate of your sequencing experiment
    • + +
  • Visualize sample diversity using Krona and Phinch
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + Go to session page. + + + + + + + + + + +
+
+
+ + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + +

In this 3-part module, you will learn about Nanopore long-read sequencing for the +detection of antimicrobial resistance (AMR). There is a short video showing you the +wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, +and finally a practical tutorial walking you through an AMR analysis in Galaxy. +

+ + + + + + + + + + + + + + + + + + +
+
+

MinION Wetlab demo (Demo)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

+
Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Antibiotic resistance detection (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + Go to session page. + + + + + + + + + + +
+
+
+ + + + + + +

Microbiome

+ + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + +

To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene +is often used. This allows us to identify the bacterial species present in our sample. +This lecture and practical session introduces you to 16S analysis in Galaxy using the +mothur tool suite. +

+ + + + + + + + + + + + + + + + + + +
+
+

Introduction to Microbiome Analysis (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
Support: + +
Learning Objectives: +
    + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

16S Microbial Analysis with mothur (short) (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:1 hour 37 minutes
Captions: Saskia Hiltemann
Created:19 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
    • + +
  • Using a mock community to assess the error rate of your sequencing experiment
    • + +
  • Visualize sample diversity using Krona and Phinch
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + Go to session page. + + + + + + + + + + +
+
+
+ + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + +

In this 3-part module, you will learn about Nanopore long-read sequencing for the +detection of antimicrobial resistance (AMR). There is a short video showing you the +wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, +and finally a practical tutorial walking you through an AMR analysis in Galaxy. +

+ + + + + + + + + + + + + + + + + + +
+
+

MinION Wetlab demo (Demo)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

+
Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Antibiotic resistance detection (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + Go to session page. + + + + + + + + + + +
+
+
+ + + + + + +

Wetlab

+ + + + + + + + + + + + + + + +
+ +
+ +
+ +
+ +
+ + + +

In this 3-part module, you will learn about Nanopore long-read sequencing for the +detection of antimicrobial resistance (AMR). There is a short video showing you the +wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, +and finally a practical tutorial walking you through an AMR analysis in Galaxy. +

+ + + + + + + + + + + + + + + + + + +
+
+

MinION Wetlab demo (Demo)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

+
Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+

Antibiotic resistance detection (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + Go to session page. + + + + + + + + + + +
+
+
+ + + + + +

Statistics

diff --git a/sessions/microbiome/mothur-miseq-sop-short/index.html b/sessions/microbiome/mothur-miseq-sop-short/index.html new file mode 100644 index 00000000..58b9fdd6 --- /dev/null +++ b/sessions/microbiome/mothur-miseq-sop-short/index.html @@ -0,0 +1,599 @@ + + + + + GTN Video: 16S Microbial Analysis with mothur (short) + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +

16S Microbial Analysis with mothur (short)

+ +Below are video tutorials for this GTN session, created for various (past) events. + +

+ +To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene +is often used. This allows us to identify the bacterial species present in our sample. +This lecture and practical session introduces you to 16S analysis in Galaxy using the +mothur tool suite. + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

Introduction to Microbiome Analysis (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:15 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Materials: + +
Support: + +
Learning Objectives: +
    + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

16S Microbial Analysis with mothur (short) (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

+
Length:1 hour 37 minutes
Captions: Saskia Hiltemann
Created:19 May 2023
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
    • + +
  • Using a mock community to assess the error rate of your sequencing experiment
    • + +
  • Visualize sample diversity using Krona and Phinch
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + +
+
+ + +
+ +
+
+

+ Logo for the Gallantries project + GTN Video Library +

+
+
+

Everyone participating is expected to abide by the Code of Conduct

+
+
+ european flag with text: With the support of the Erasmus+ Programme of the European Union. +
+
+ This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. + +
+ +
+ + + + diff --git a/sessions/microbiome/nanopore/index.html b/sessions/microbiome/nanopore/index.html new file mode 100644 index 00000000..7fc3b305 --- /dev/null +++ b/sessions/microbiome/nanopore/index.html @@ -0,0 +1,708 @@ + + + + + GTN Video: microbiome/nanopore + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +

+ +Below are video tutorials for this GTN session, created for various (past) events. + +

+ +In this 3-part module, you will learn about Nanopore long-read sequencing for the +detection of antimicrobial resistance (AMR). There is a short video showing you the +wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, +and finally a practical tutorial walking you through an AMR analysis in Galaxy. + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

wetlab/miseq (Demo)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

+
Length:20 minutes
Captions: Saskia Hiltemann
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

microbiome/clinical-applications (Lecture)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

+
Length:30 minutes
Captions: Helena Rasche
Created:15 February 2021
Support: + +
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

Antibiotic resistance detection (Tutorial)

+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

+
Length:45 minutes
Captions: Bérénice Batut
Created:15 February 2021
Materials: + +
Support: + +
Supported Servers: + + + + + Known Working + + + + + Possibly Working + + +
Learning Objectives: +
    + +
  • Perform Quality control on your reads
    • + +
  • Assemble a genome with Minimap2/Miniasm/Racon
    • + +
  • Determine the structure of the genome(s)
    • + +
  • Scan for antimicrobial resistance genes with Staramr
    • + +
+
+ +
+ + Go to the video page to see all versions. + +
+ + + + +
+

Speaker

+ + + + + + + + +
+ + + + + + +
+ +
+ + +
+ + + + + + + + +
+
+ + + +