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Bioinformatics training

Training in Basic Bioinformatics, Nextflow and Apptainer (Singularity) usage, and GEN-ERA Workflow for Microbial Genomics

This course teaches the basics of the Linux command line and HPC cluster utilization. The usage of the Apptainer container and Nextflow workflow will be taught. The BCCM bioinformatic toolbox for microbial genomics (GEN-ERA) will be covered through theoretical and practical exercises. The course covers genome assembly (short and long reads), metabolic modelling, phylogenomics, and the generation of ANI matrices. A focus will be placed on cyanobacterial genomics.

  • Level: beginners
  • Materials: A Unix or Windows laptop (sessions on the HPC cluster will be provided)
  • Outcomes: Participants will acquire the ability to utilize public Nextflow workflows and Apptainer containers, enabling them to conduct genomic analyses on bacterial genomes.

The training takes place at ULiege (Campus Sart Tilman, Liège, BE) and is offered in English or French, depending on the participants.

For more information, please contact us.

  Duration: 5 days
 
Next sessions: on request
 
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Training on Nextflow and Singularity (Apptainer) workflow development

This course teaches how to develop Nextflow workflow and Singularity containers (Apptainer), and connect the two tools to create a fully reproducible workflow. The Nextflow portion, covering processes and channels, will be taught using Bash scripting, and no prior knowledge is required. This 4-day course covers the following topics:

  • The use of Unix and basic command-line operations in Bash
  • Utilization of Nextflow and Singularity
  • Creation of Singularity containers
  • Development of Nextflow workflows

Course details:

  • Level: beginners
  • Materials: A Unix or Windows laptop (sessions on the HPC cluster will be provided)
  • Outcomes: Participants will acquire the ability to develop their own reproducible workflows.

The training takes place at ULiege (Campus Sart Tilman, Liège, BE) and is offered in English or French, depending on the participants.

For more information, please contact us.

  Duration: 4 days
 
Next sessions: on request
 
Ask a quote