Keywords: assembly, ecology, galaxy-interface, introduction, microbiome, one-health, proteomics, single-cell, statistics

Learning objectives:

• Assess long reads FASTQ quality using Nanoplot and PycoQC
• Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
• Become comfortable converting text-based files in a variety of ways.
• Connect different parts of the Research Object using identifiers
• Construct an RO-Crate by hand using JSON
• Describe each part of the Research Object
• Explain what is a BAM file and what it contains
• Familiarize yourself with data manipulation tools in Galaxy
• Familiarize yourself with the basics of Galaxy
• Gain understanding on navigating and manipulating histories
• Generate a workflow test using Planemo
• Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with Plasmodium
• Learn basic JSON-LD to create FAIR metadata
• Learn how histories work
• Learn how to create a workflow
• Learn how to extract and run a workflow
• Learn how to obtain data from external sources
• Learn how to run tools
• Learn how to share a history
• Learn how to share your work
• Learn how to upload a file
• Learn how to use a tool
• Learn how to view histories
• Learn how to view results
• Perform basic text manipulation tasks in Galaxy
• Perform quality correction with Cutadapt (short reads)
• Process single-end and paired-end data
• Reason about the expected outcome of tools
• Run a tool to map reads to a reference genome
• Summarise quality metrics MultiQC
• Understand and master dataset collections
• Understand how testing can be automated with GitHub Actions
• Understand most common types of NGS-related datatypes
• Use genome browser to understand your data

Organizer: Anika Erxleben (https://orcid.org/0000-0002-7427-6478), Anna Syme (https://orcid.org/0000-0002-9906-0673), Anton Nekrutenko (https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/), Dannon Baker (https://training.galaxyproject.org/training-material/hall-of-fame/dannon/), Delphine Lariviere (https://orcid.org/0000-0001-6421-3484), Gareth Price (https://training.galaxyproject.org/training-material/hall-of-fame/GarethPrice-Aus/), John Davis (https://orcid.org/0000-0002-1363-1245), Michael Schatz (https://training.galaxyproject.org/training-material/hall-of-fame/mschatz/), Natalie Kucher (https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/), Natalie Whitaker-Allen (https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/), Saskia Hiltemann (https://orcid.org/0000-0003-3803-468X), Teresa Müller (https://orcid.org/0000-0003-1252-9684)

Event types:

• Workshops and courses

Sponsors: ABRomics, ELIXIR Europe, German Network for Bioinformatics Infrastructure Service, Training, Cooperations & Cloud Computing, Institut Français de Bioinformatique, Ministry of Science, Research and Arts

Instructors: Ahmed Hamid Awan, Anika Erxleben, Anna Syme, Anup Kumar, Anthony Bretaudeau, Bérénice Batut, Björn Grüning, Clea Siguret, Dannon Baker, Diana Chiang Jurado, Deepti Varshney, Delphine Lariviere, Eli Chadwick, Engy Nasr, Emmanuel Augustine, Gareth Price, Igor Makunin, John Davis, Lucille Delisle, Matthias Bernt, Melanie Föll, Michael Schatz, Natalie Whitaker-Allen, Nate Coraor, Paul Zierep, Pavankumar Videm, Polina Polunina, Pratik Jagtap, Rand Zoabi, Romane LIBOUBAN, Saim Momin, Stéphanie Robin, Subina Mehta, Teresa Müller, Timothy J. Griffin, Tyler Collins, Wendi Bacon, Wolfgang Maier

Scientific topics: Mapping