Introduction to Snakemake
Learn Snakemake to automate data workflows. Build reproducible, scalable pipelines for research with hands-on training in this 4-day live online course.
Duration: 4 Days, 3 hours per day
Next Date: October 6-17, 2025
Format: Live Online Format
UK (GMT) local time - All sessions will be recorded and made available to ensure accessibility for attendees across different time zones.
£350Registration Fee
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- Overview
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Course Description
Researchers needing to implement data analysis workflows face a number of common challenges, including the need to organise their tasks, make effective use of compute resources, handle unexpected errors in processing, and document and share their methods. The Snakemake workflow system provides effective solutions to these problems. By the end of the course, you will be confident in using Snakemake to tackle complex workflow problems and in your day-to-day research. Whilst the software used in the workshop from the domain od genomics, the principles can be applied to ay field.
What You’ll Learn
During the course will cover the following:
- Why automated workflows are an powerful tool for any data analysis project
- The basic principles behind snakemake
- Considerations when building more complex workflows
- How to effectively trouble shoot you snakemake workflow
- How to make sure you can incorporate any requiered program into your workflow.
- How to efficiently restart partially completed workflows
- How to configure your workflows
Course Format
Interactive Learning Format
Each day features a well-balanced combination of lectures and hands-on practical exercises, with dedicated time for discussing participants’ own data, time permitting.
Global Accessibility
All live sessions are recorded and made available on the same day, ensuring accessibility for participants across different time zones.
Collaborative Discussions
Open discussion sessions provide an opportunity for participants to explore specific research questions and engage with instructors and peers.
Comprehensive Course Materials
All code, datasets, and presentation slides used during the course will be shared with participants by the instructor.
Personalized Data Engagement
Participants are encouraged to bring their own data for discussion and practical application during the course.
Post-Course Support
Participants will receive continued support via email for 30 days following the course, along with on-demand access to session recordings for the same period.
Who Should Attend / Intended Audiences
This course is intended for researchers who need to automate complex, multi-step data analysis tasks. Participants should have a working knowledge of the Linux BASH command line. While Snakemake workflows are written in a Python-based language, no prior knowledge of Python is required.
Equipment and Software requirements
A laptop or desktop computer with a reasonable internet connection and a webrowser. No other software is required.
While not essential, using a large monitor – or ideally a dual-monitor setup – can significantly enhance your learning experience by allowing you to view course materials and work in R or linux simultaneously.
A working webcam is recommended to support interactive elements of the course. We encourage participants to keep their cameras on during live Zoom sessions to foster a more engaging and collaborative environment.
All necessary software is installed already on a virtual machine that you will access through your web browser
Dr. Frances Turner
Frances is a bioinformatician at Edinburgh University with extensive experience supporting researchers across the life sciences in analysing and interpreting high-throughput sequencing data. Her work focuses on developing and applying bioinformatics pipelines and analytical approaches that enable scientists to extract meaningful biological insights from complex genomic datasets. She works with a wide range of sequencing applications, including whole-genome, transcriptome, and metagenomic data, and has particular expertise in ensuring data quality, reproducibility, and effective downstream analysis.
Frances has spent many years collaborating closely with research groups from diverse disciplines, providing both technical expertise and strategic advice on study design, sequencing strategy, and data interpretation. Alongside her consultancy and applied work, she is also committed to training and knowledge exchange, delivering workshops and guidance to help life scientists build confidence in handling and analysing their own sequencing data.
Education & Career
- PhD in Bioinformatics
- MSc Bioinformatics
- Bioinformatician at Edinburgh University, providing analysis support and training for high-throughput sequencing projects at the Gene Therapy Mission Hub.
Research Focus
Frances’ work centres on enabling researchers to make the most of next-generation sequencing technologies. She is particularly interested in:
- Developing and refining bioinformatics workflows for diverse sequencing applications
- Supporting reproducible and scalable approaches to data analysis
- Bridging the gap between experimental design and downstream interpretation
Current Projects
- Providing end-to-end analysis support for whole-genome, transcriptomic, and metagenomic studies
- Collaborating with life science researchers on custom data workflows
- Contributing to training programmes that build bioinformatics capacity in the research community
Professional Consultancy
Frances provides expert bioinformatics support to academic and applied research projects, offering guidance on sequencing design, data processing, and statistical interpretation. She regularly collaborates with interdisciplinary teams, ensuring robust, reproducible, and biologically meaningful outcomes.
Teaching & Skills
- Teaches workshops on sequencing data analysis, quality control, and reproducible pipelines
- Skilled in a wide range of bioinformatics tools and platforms for genomic and transcriptomic analysis
- Advocates for open science, reproducibility, and empowering life scientists to engage confidently with their data
Links
• LinkedIn
Session 1- 01:30:00 – What is snakemake?
An overview of snakemake and a look at a very simple example
Session 2 – 01:30:00 – Making your workflow reusable
Understanding how to allow your workflow to applicable to new datasets using place holders and wildcard
Session 3 – 01:30:00 – Chaining rules
Understanding how to expand your workflow to handle multi-step analysis.
Session 4 – 01:30:00 -Complex outputs, logs and errors
Understanding how to incorporate programs with more complex outputs, and how to trouble shoot this process
Session 5 – 01:30:00 How Snakemake plans its jobs?
Understand how to visualise a snakemake workflow, how snakemake avoids repeating unnecessary steps, and how you can control which step snakemake re-runs.
Session 6 – 01:30:00 – Processing lists of inputs
Understanding how to easily run a snakemake workflow on a whole list of datasets
Session 10 – 01:30:00 -Handling awkward programs
Understanding why the convention used by some programs to in the naming of input or output files can mean a little extra thought Is required to incorporate them in to a snakemake workflow, and approaches to deal with this.
Session 11 – 01:30:00 – Configuring workflows
Understanding how to add configuration files to make your workflows even more flexible and easy to use
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Frequently asked questions
Everything you need to know about the product and billing.
When will I receive instructions on how to join?
You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.
Do I need administrator rights on my computer?
I’m attending the course live — will I also get access to the session recordings?
I can’t attend every live session — can I join some sessions live and catch up on others later?
I’m in a different time zone and plan to follow the course via recordings. When will these be available?
I can’t attend live — how can I ask questions?
Will I receive a certificate?
When will I receive instructions on how to join?
You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.
Do I need administrator rights on my computer?
I’m attending the course live — will I also get access to the session recordings?
I can’t attend every live session — can I join some sessions live and catch up on others later?
I’m in a different time zone and plan to follow the course via recordings. When will these be available?
I can’t attend live — how can I ask questions?
Will I receive a certificate?
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