• Header of Genetics and Genomics at Transmitting Science

Live Online Course – 2nd edition

Introduction to transposable element detection using sequencing data

October 12th-20th, 2023

Live sessions will be recorded

Course Introduction to transposable element detection using sequencing data


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Course Overview & Programme

Transposable elements (TEs) can be major components of eukaryotic genomes. Such repeated sequences, which can make up very large proportions like about 50% of mammalian genomes to more than 80% in the genomes of some plants, can promote various types of mutations, from gene interruption and expression alteration to large-scale chromosomal rearrangements. They can also promote the formation of new genes. Despite their deleterious effects, TEs are currently considered as major actors in genome evolution due the genetic and epigenetic diversity they can generate.

Even if they have a fundamental biological role, detection and analysis of TE sequences are still technologically challenging. The length and quality of sequenced reads make their detection and annotation difficult (40% detection error). Moreover, the presence of TEs in a genome can also lead to important assembly errors due to rearrangement and the merge of repeats, and to difficulties in the identification of splicing events and in the estimation of gene expression in transcriptomic analyses. It is thus important to be able to identify these sequences in genomic and transcriptomic data.

Since several years, a large number of bioinformatic tools have been developed allowing a better identification of TEs in genomes. New tools are released regularly to follow the progress of sequencing technologies but also to answer particular biological questions allowing to go from the TE annotation in assembled or unassembled genomes, to insertion polymorphism detection in natural populations. The result is a particularly large choice for users leading to difficulties in the determination of the best tool(s) to use according to the case.

In this course, we aim at proposing an introduction of selected bioinformatic tools for the detection and analysis of TEs in genomic data (RepeatMasker, DnaPipeTE, T-lex).

  • Introduction to the Linux Operating System
    • First contact with the shell (Bash Terminal)
    • Basic command lines
    • File system (ftp/ssh protocols)
    • Text editors (emacs, notepad)
    • Working with text files with commands such as grep, sed , tr and awk
  • Introduction on TE biology
    • TE discovery
    • TE classification
  • Enforcement to solve common problems in bioinformatics
    • Analysis of sequences – Fasta format
    • Look for particular patterns in TE sequences ( LTR, TIR or TSD)
    • Parsing common annotation files (gff,bed,vcf)Tuesday, June 15th, 2019
  • How to detect TE in assembled genomes?
    • Annotation of TE families using de novo approaches
    • Detection and annotation of individual TE insertions
  • Application by group: TE annotation in Drosophila
    • RepeatMasker presentation and command line
    • How to interpret the RepeatMasker outputs
    • How to parse the RepeatMasker output (OneCodeTofindThemAll)
  • Each group present their RepeatMasker results
  • Introduction to the next-generation sequencing
    • Sequencing technologies
    • Sequencing data – Fastq format
  • Discussions : Not all TE insertions are part of the assembly?
  • Application by group: TE families detection in Drosophila
    • DNAPipeTE presentation and command line
    • How to interpret the DNAPipeTE outputs
  • Each group present their own results
  • Sequencing projects – Population genomics projects: case of DGRP
  • Presence/absence calls of previously detected TE insertions
    • T-lex presentation and command line
    • How to interpret the T-lex output
  •  Each group present their own results
  • Do not forget the novel TE insertions
    • General approach
    • McClintock presentation and command line
    • How to interpret the McClintock output
  • Application by group: de novo TE detection in Drosophila using DGRP data
  • Each group present their own results
  • The advantages of the long-read sequencing technology
  • Questions

Participants must have a personal computer (Windows, Mac, Linux) and access to a good internet connection. The use of a webcam and headphones is strongly recommended.

Participants should be familiar with Bash and the use of command lines.

All participants must install on their own personal laptop the following software: Putty (Windows only) and Filezilla.


Anna-Sophie Fiston-Lavier instructor for Transmitting Science

Dr. Anna-Sophie Fiston-Lavier

Institut des Sciences de l’Evolution de Montpellier

Emmanuelle Lerat instructor for Transmitting Science

Dr. Emmanuelle Lerat

Université Lyon 1

Dates & Schedule

Online live sessions on 12th, 13th, 18th, 19th, and 20th of October

From 13:00 to 17:00 (Madrid time zone)

Total course hours: 25

20 hours of online live sessions, plus 5 hours of participants working on their own on tutored exercises.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.



This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom and tasks to be completed in between live sessions on the Slack platform.
Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.


Places are limited to 20 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until August 31st, 2023):
  • 546 €
    (436.80 € for Ambassador Institutions)
  • Regular (after August 31st, 2023):
  • 646 €
    (516.80 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.