Tag - Genome annotation

24-28 Sep 2018, France

A course is being organized in Montpellier, hosted by the French ELIXIR Node and in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and annotation experts in Europe will be teaching at the course.

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue to step-by-step describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.

Prerequisites:

• knowledge of using command line Linux
• prepare info about your own project and tentatively bring your own data

University of Tromsø
Medisin og helsefagbygget: Datarom (U7.110)
Tuesday 26th November 09.00-15.00

We are pleased to announce the second hands-on bioinformatics NeLS workshop organised in Tromsø by ELIXIR Norway (https://www.elixir-norway.org/).  The topic is on how you can use the Norwegian e-Infrastructure for Life Sciences (NeLS) (nels.bioinfo.no) to store and share data, and to run analyses via customisable analysis workflows in Galaxy. More specifically, we will go through how you can store data in NeLS and upload it directly into Galaxy. We will also construct and run a complete sequence analysis workflow for taxonomic profiling on a metagenomic sample.  There are no requirements for programming skills or experience using the command line, as Galaxy provides a web interface for running analysis.

Teachers:
    Erik Hjerde, University of Tromsø
    Ståle Nygård, University of Oslo
    Nils Peder Willassen, University of Tromsø

ELIXIR TtR course: Basic genomics using advanced analysis tools

Genomic Data Science with Galaxy

Dec 20-21, University of Ljubljana, Faculty of Medicine, Ljubljana (Slovenia)

Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy Platform provides user friendly software for producing reproducible genomic pipelines for data analysis. This workshop will provide a 2 day introductory session to Galaxy software system.

The course will be in English.

Registration:

• register here
• the limit of participants is 20
• the course is free of charge

This course will focus on introducing the Galaxy user interface and how it can be used for basic genomic analyses. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy.

Program topics:

• Quick introduction to Galaxy GUI
• From peaks to genes
  
• Reference-based RNA-seq - Quality control
• Reference-based RNA-Seq - Sequencing
  

Lecturers will be Christophe Antoniewski and Olivier Inizan from ELIXIR France.

Course is organised by ELIXIR Slovenia in collaboration with ELIXIR France.

ELIXIR is an European ESFRI priority research infrastructure for bioinformatics that provides databases, (software) tools, services and training (including training materials) for information, cloud storage and supercomputers in the area of life sciences. It coordinates, develops, integrates and sustains life science (bioinformatics) resources across Europe.

Prerequisites:

• Wi-Fi enabled laptop with a modern web browser. Latest versions of Google Chrome, Firefox, Safari and Opera will work best.