All exercises
Getting started
Prepare the exercise data, computing environment and analysis record before running a workflow.
Read guideParticipant documentation
How to approach the exercises
Prepare your data, choose a reproducible workflow, review the biological evidence and return a valid result sheet. Start with the general guide, then open the page for your exercise.
All exercises
Installing bioinformatics tools
Set up reproducible Pixi, Conda, Docker, Nextflow or Apptainer environments before starting an exercise.
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Short-read assembly
Inspect paired-end reads, assemble each bacterial genome and return a defensible species and QC result.
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Hybrid assembly
Combine short and long reads, assess polishing and decide whether each assembly is complete or fragmented.
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Genotyping
Run Kleborate on supplied assemblies and return consistent species, sequence-type, surface-locus and resistance calls.
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Outbreak analysis
Inspect reads, call variants against one reference, infer a phylogeny and assign analytical clusters.
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Submission and troubleshooting
Record provenance, validate the result sheet and diagnose common workflow failures.
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