On-Site NGS Bioinformatics Training
Tailored hands-on courses that help your team understand, run and critically evaluate NGS data analysis workflows.
ecSeq brings practical NGS bioinformatics training directly to your institute, university, company or clinical research environment. We design the course around your team, your scientific questions, your experience level and your technical environment. Topics can range from FASTQ quality control, read mapping and variant calling to RNA-seq, single-cell RNA-seq, epigenomics and reproducible pipeline development with Nextflow.
Designed and taught by experienced bioinformaticians who work on real NGS projects, data analyses and software pipelines.
Build NGS bioinformatics competence inside your team
Many teams can now generate sequencing data quickly, but the real bottleneck is often the analysis: understanding file formats, judging data quality, choosing the right workflow, recognizing artefacts and interpreting results with confidence. Our on-site courses are designed to close this gap.
Choose the format that fits your team
Research groups and company teams often need different types of on-site training. The general concept is the same: practical, hands-on NGS bioinformatics training. The motivation, course design and level of technical depth can be very different.
For PhD and research groups
For doctoral programmes, research groups, collaborative projects and wet-lab teams that want to build practical NGS data analysis skills together.
- Ideal for groups of 10-25 participants
- Hands-on training instead of passive online lectures
- Shared learning, discussion and group interaction
- No travel and accommodation costs for all participants
- Useful when no bioinformatics core facility is directly available
For biotech and pharma teams
For companies that have built a bioinformatics, data science or computational biology group and now need to enter NGS quickly and in a structured way.
- Fast onboarding into NGS as a new data type
- Training focused on relevant assays and workflows
- Discussion of infrastructure and technical constraints
- Pipeline thinking, reproducibility and Nextflow options
- Better communication between bioinformatics, wet lab and project teams
Why ecSeq?
ecSeq is not a pure training company. We analyze NGS data, develop bioinformatics software, build reproducible pipelines and support real research, biotech and diagnostic projects. This practical background is reflected in our courses: we do not only explain which command to run, but why a step is needed, what can go wrong, how quality can be assessed and how results should be interpreted.
This is especially important for teams that need more than a theoretical introduction. A good on-site course should help participants develop judgment: when to trust an analysis, when to question it and when to ask for deeper bioinformatics support.
Training paths that can be adapted to your team
We combine proven ecSeq course modules into a customized on-site curriculum. The training can be introductory, application-specific, pipeline-oriented or focused on the workflows most relevant to your team.
NGS Data Analysis Essentials
A practical starting point for teams that want to understand how sequencing data is processed and assessed.
- Linux and command-line basics
- FASTQ files and quality control
- Adapter clipping and trimming
- Read mapping and BAM/SAM files
- Genome browser inspection and mapping statistics
Typical duration: 2-3 days
Variant Calling and VCF Interpretation
For teams that need to understand DNA sequencing workflows, variant calling results and practical quality filters.
- Read alignment and coverage
- Variant calling concepts
- VCF structure and quality fields
- Variant filtering and annotation
- Interpretation limits and common artefacts
Typical duration: 1-3 days
Bulk RNA-Seq Data Analysis
From raw RNA-seq reads to expression quantification, differential expression and biological interpretation.
- RNA-seq experimental design and QC
- Read alignment or transcript quantification
- Gene and transcript count tables
- Differential expression with Bioconductor
- Diagnostic plots, batch effects and interpretation
Typical duration: 2-4 days
Single-Cell RNA-Seq Analysis
For teams that generate or receive single-cell data and want to understand the decisions behind the plots.
- 10x Genomics and Cell Ranger outputs
- Count matrices and single-cell QC
- Seurat-based analysis workflows
- Dimensionality reduction, clustering and marker genes
- Cell type annotation, integration and batch effects
Typical duration: 3 days
NGS Pipeline Development with Nextflow
For computational teams that want to move beyond one-off scripts and build reproducible analysis workflows.
- Nextflow processes, channels and parameters
- Containers and reproducible software environments
- Local, HPC and cloud execution profiles
- Debugging, reporting and workflow structure
- From scripts to maintainable team workflows
Typical duration: 3 days
NGS Epigenomics
Practical analysis of regulatory NGS assays, from quality control to genome browser interpretation.
- Bisulfite sequencing and DNA methylation
- ChIP-seq and ATAC-seq analysis concepts
- Peak files, methylation calls and DMRs
- Visualization in genome browsers
- Integration with gene expression and annotation data
Typical duration: 2-4 days
How we design your on-site course
Scoping
We discuss your team, scientific background, experience level, data type, available infrastructure and training goals. This helps us define whether the course should be introductory, application-specific, pipeline-oriented or focused on selected workflows relevant to your team.
Curriculum design
We combine suitable modules from our established NGS workshops and adapt them to your group. A doctoral research group without bioinformatics support needs a different course structure than a pharma data science team entering NGS.
Technical preparation
We define the setup for the hands-on sessions. Depending on the course, we use carefully prepared ecSeq training datasets, suitable example workflows, your infrastructure where appropriate, cloud systems or preconfigured training environments.
Hands-on training
The course combines short theory blocks with guided practical exercises. Participants do not only see analysis results; they learn how results are generated, checked and interpreted.
Handover and next steps
Participants receive course materials, example commands, training results and practical guidance for continued work. If needed, the training can be followed by project-specific consulting, workflow review or custom pipeline development.
What your team will take home
The goal is not to memorize commands. The goal is to understand what the analysis is doing, when to trust the output and when to question it.
- Practical experience with real NGS tools
- Reusable course materials and example workflows
- Better understanding of FASTQ, BAM, VCF and count matrices
- Ability to interpret QC reports and mapping statistics
- Awareness of common artefacts and analysis pitfalls
- Clearer communication with sequencing providers and collaborators
- Project-specific discussion of analysis strategies and workflow choices
- Foundations for reproducible analysis workflows
- Improved confidence in planning and evaluating NGS projects
- Certificate of participation upon request
From training to implementation
Some teams use an on-site course as a focused training event. Others use it as the starting point for a larger internal NGS strategy. We can therefore keep the training self-contained or connect it to follow-up activities.
Training only
Build a shared understanding of NGS data analysis, file formats, QC, workflows and interpretation.
Training plus project clinic
Add structured discussion of your analysis goals, workflow choices, QC strategies or planned experiments.
Training plus pipeline project
Continue with workflow review, Nextflow implementation, pipeline refactoring or custom NGS software development.
Experienced by participants from academia, biotech and pharma
Participants in ecSeq NGS workshops have come from organizations such as Pfizer, AstraZeneca, Sanofi, NIBR - Novartis Pharma AG, Roche Diagnostics GmbH, Bayer, Bayer Crop Science, Max Delbrück Center for Molecular Medicine, Max Planck Institute for Biology of Ageing, University of Vienna, Hannover Medical School, San Raffaele Hospital, the German Federal Institute for Risk Assessment and many other universities, hospitals, research institutes and companies.
Not sure which format fits your team?
Tell us about your data type, group size, experience level and training goal. We will suggest a realistic on-site training structure that fits your team, your infrastructure and your scientific question.
