France
Tutorial, Training materials, Bioinformatics
How to use REPET software for de novo annotation of transposable elements in genomes
This practical training was presented in the 11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in 2023 (http://repeatexplorer.org/?page_id=14).
The objective of this practical training is to have the basics for using the REPET software to be able to annotate transposable elements of a genome.
This tutorial uses the Docker image of REPET software (https://hub.docker.com/r/urgi/docker_vre_aio).
The test dataset used is Drosophila melanogaster chromosome 4 and the duration of the practical training is about 2-3 hours.
DOI: Johann Confais. Practical training III : REPET pipeline. 11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis, Laboratory of Molecular Cytogenetics of the Biology Centre CAS, May 2023, České Budějovice, Czech Republic. (https://hal.science/hal-04117938)
Licence: Creative Commons Attribution Non Commercial No Derivatives 4.0 International
Contact: [email protected]
Keywords: Transposons, Annotation, Pipelines, Docker
Target audience: Scientists, Bioinformatician, Biologists, Genomicists, Computer Scientists
Resource type: Tutorial, Training materials, Bioinformatics
Status: Active
Prerequisites:
You need to have a working environment that allows the use of Docker technology.
Learning objectives:
The objective of this practical training is to have the basics for using the REPET software to be able to annotate transposable elements of a genome.
Date created: 2023-05-25
Contributors: INRAE
Scientific topics: Genomics, Structural variation, Bioinformatics
Operations: Genome annotation, Sequence classification
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