Managing Bioinformatics Software and Pipelines

About the course  |  Intended audience  |  Prerequisites  |  Content details  |  Scheduled events

About the course

Setting up a computer environment for bioinformatics analysis can be challenging. Most bioinformatics applications rely on multiple software packages and involve complex data processing pipelines. This course introduces the computational tools that simplify software management and enable reproducible, automated analyses.

Participants will learn how to use package managers, software containers, and workflow management systems to install, configure, and run bioinformatics pipelines. Examples are drawn from a range of applications, including RNA-seq, ChIP-seq, variant calling, and viral genomics.

The focus of the course is on using existing computational tools and community-developed workflows rather than on the details of specific bioinformatics analyses or developing new pipelines and containers.

By the end of the course, participants should be able to confidently manage software environments and execute bioinformatics workflows on both local computers and High Performance Computing (HPC) systems.

Teaching is primarily hands-on, with short presentations and demonstrations introducing the concepts and tools needed to manage and automate bioinformatics analyses.

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Intended audience

This course is suitable for:

  • researchers who are starting to run bioinformatics analyses independently
  • participants attending training courses on specific bioinformatics applications, such as RNA-seq, ChIP-seq, and variant calling
  • HPC users who want to learn how to manage software and automate and parallelise analyses using existing pipelines

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Prerequisites

Participants should have:

  • a working knowledge of the UNIX command line
  • a basic understanding of high-throughput sequencing technologies

The following experience is recommended:

  • working on High Performance Computing (HPC) systems using SLURM
  • familiarity with the data processing steps for at least one omics application, such as RNA-seq, ChIP-seq, variant calling, bacterial genomics, or metagenomics

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Content details

The course covers the following topics:

  • Package managers
    Introduces package managers and their role in installing and maintaining complex software environments for bioinformatics analyses. Participants learn how to create and manage software environments using conda and mamba.
  • Software containers
    Introduces software containers as a solution to software dependency and reproducibility challenges. Participants learn how to search for and use software images and run commands within containers using Singularity.
  • Workflow management
    Introduces workflow management systems and the benefits of automated and reproducible data processing pipelines.
  • Community-developed workflows
    Covers the use of workflows developed and maintained by the bioinformatics community. Participants learn how to search for nf-core workflows and use their documentation to configure analyses.
  • Executing workflows with Nextflow
    Introduces the Nextflow workflow manager and demonstrates how to execute workflows on both local computers and remote High Performance Computing systems.
  • Running workflows on HPC systems
    Covers the practical aspects of configuring and running Nextflow workflows on HPC infrastructure, including automating and parallelising analyses.

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