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Essential command line bioinformatics and genome analysis

BSI training
DNA genome sequencing concept
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Bioinformatics is now a potent driver of scientific development, complementing wet-lab research in immunology and becoming an essential skill for current and future generations.

The British Society for Immunology offers highly rated online training to equip wet-lab life scientists with the skills and confidence to perform their own bioinformatic data analysis.

‘Essential command line bioinformatics & genome analysis’ is an advanced course designed for wet-lab immunologists, biologists and other life scientists who have some experience* and would like an in-depth course to:

  • Learn how to code in the command line and create omic alignment and processing pipelines for any dataset
  • Explore their own genomic or epigenomic datasets
  • Or take the next essential step in becoming a bioinformatician
Do you want to better understand the data processing side of sequencing analysis and raise the impact of your research? Learn in six online sessions!

This course forms part of a wider bioinformatics training programme, developed and delivered by the Glasgow Bioinformatic Core and offered by the BSI.

Course description

Starting on Monday 29 July 2024, this top-rated course takes place each Monday (9:30–12:30 and 13:30–16:30 BST) until 2 September.

It covers Linux and the command line, plus all of the typical tools and pipelines used in command-line omics, particularly genomics. This includes:

  • The Linux environment and command-line coding
  • Sequence alignment using BLAST, Bowtie2 and Kallisto
  • QC of sequence data
  • Writing pipelines
  • How to call polymorphisms and mutations, and visualising them in R (circos, oncoplot)
  • Generating and visualising phylogenetic trees
  • ChIP-seq and ATAC-seq
  • RNA-seq alignment

It consists of six online sessions in total. After the third day, you can skip any of the following sessions if the topic isn’t relevant to you. You can take a look at the course outline here.

The course is delivered by John J. Cole, Manager of the Glasgow Bioinformatic Core, and his team of seasoned demonstrators. John’s background as a wet-lab biologist and decades of experience as a bioinformatician and lecturer perfectly positions him to help you master bioinformatics and R skills.

You will get:

  • Digestible classes that fit around your lab schedule – just one day a week on Zoom
  • Low-cost training, significantly more affordable than other courses – only £325+VAT for BSI members 
  • Sought-after skills that will expand your career prospects – add it to your CV!
  • Confidence to carry out bioinformatic data processing and analysis of your own, or public datasets
  • Skills to perform regular omic analysis of your own datasets and genomics or epigenomics with the command line

And much more! Here you can download the course outline


Registration is now open.

BSI member£325 + VAT (£390 total)
Non-member  £650 +VAT (£780 total)

The British Society for Immunology offers this course at a discount to all BSI members. You can sign up to become a member online. BSI members also benefit from discounts on fees for BSI events, as well as free access to our journals, grants, career development activities and much more.

Rating and reviews

This highly rated programme has had over 1,200 attendees since 2020, with a mean rating of 9.4/10 for content and delivery, and 93% of participants thinking the session length and pace was “about right”, after 332 reviews.

Who signs up for this training?

Wet-lab scientists…

  • Who have attended the first course ‘Omic data analysis and visualisation using R’ or have a comparable level of experience
  • Doing or planning on doing an omic experiment as part of a project
  • Planning to analyse omic datasets regularly throughout their future career
  • Exploring or planning to explore their own genomic or epigenomic datasets
  • Keen to learn R and bioinformatics to advance their career, for example after finishing a PhD or in future post-docs
  • Who need to understand omics in the current literature

Other courses in this training programme

This training programme has several courses, depending on need and experience, starting with an essential course for complete beginners to set the foundations and building on those skills to help you on specific experiments. For example, allowing for specialisation into advanced topics such as single-cell RNA-sequencing. Here you can see the full outline of the programme and guidance on which course is right for you

Glasgow Bioinformatic Core Logo

The programme has been developed and is delivered by the Glasgow Bioinformatic Core and is being offered by the British Society for Immunology.