Module: Genome Annotation
This module will cover genome annotation analysis in Galaxy
This tutorial will introduce genome annotation process and give you hands-on experience with annotating a prokaryotic genome using Prokka.
Genome annotation with Prokka (Lecture)
| Description: | Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements. |
| Length: | 3 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Slides:
Genome annotation with Prokka (Tutorial)
| Description: | In this tutorial we will use Prokka to annotate a draft genome sequence. Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Prokka can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats.” |
| Length: | 20 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Supported Servers: | Known Working Possibly Working |
| Learning Objectives: |
|
Tutorial:
Speaker
This session will introduce the Apollo genome annotation platform, and provide you hands-on experience with using Apollo in Galaxy.
Refining Genome Annotations with Apollo (prokaryotes) (Lecture)
| Description: | This lecture gives a quick overview of Apollo |
| Length: | 5 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Refining Genome Annotations with Apollo (prokaryotes) (Tutorial)
| Description: | In this tutorial you will get some hands-on experience using Apollo in Galaxy |
| Length: | 1 hour |
| Captions: | Anthony Bretaudeau |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Supported Servers: | Possibly Working |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | The aim of repeat masking is to identify the location of all repeated elements along a genome sequence. Other tools (like annotation pipelines) can then take this information into account when producing their results. |
| Length: | 18 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 10 May 2023 |
| Materials: |
|
| Support: | |
| Supported Servers: | Known Working |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved. In this tutorial we will use a software tool called Funannotate (Palmer and Stajich 2020) to annotate the genome sequence of a small eukaryote: Mucor mucedo (a fungal plant pathogen). |
| Length: | 1 hour 10 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 12 May 2023 |
| Materials: |
|
| Support: | |
| Supported Servers: | Known Working Possibly Working |
| Learning Objectives: |
|
Speaker
Visualisation
Circos (Krzywinski et al. 2009) is a software package for visualizing data in a circular layout. This makes Circos ideal for exploring relationships between objects or positions. Circos plots have appeared in thousands of scientific publications. Although originally designed for visualizing genomic data, it can create figures from data in any field.
Visualisation with Circos (Lecture)
| Description: | Circos is a popular tool for creating circular graphs to display genomic data. This video will introduce this tool and how to use it within Galaxy |
| Length: | 6 minutes |
| Captions: | Assunta DeSanto, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Visualisation with Circos (Tutorial)
| Description: | Circos is a popular tool for creating circular graphs to display genomic data. This video will introduce this tool and how to use it within Galaxy |
| Length: | 50 minutes |
| Captions: | Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Alireza Khanteymoori |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Supported Servers: | Known Working Possibly Working |
| Learning Objectives: |
|
Vertebrate Genome Project
Demo Video
| Description: | This demo walks you through running the VGP Genome Assembly workflows, rather than the whole tutorial (as most GTN videos do) |
| Length: | 10 minutes |
| Captions: | Delphine Lariviere |
| Created: | 13 March 2022 |
| Materials: |
|
| Support: |
VGP assembly pipeline: Step by Step
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: | VGP assembly pipeline: Step by Step |
| Material: | GTN Tutorial |
| Support: |
Instructor
TnSeq
Essential genes detection with Transposon insertion sequencing
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: | Essential genes detection with Transposon insertion sequencing |
| Material: | GTN Tutorial |
| Support: |