Genomic processing and analysis pipeline

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English version of the Czech case export: IMTM built a national-scale Czech genome resource (ENIGMA) from 700 donor genomes using Floxgen Aggregation.

01 —

The Task

Context

The Institute of Molecular and Translational Medicine (IMTM) set out to build a comprehensive Czech genome database under the ENIGMA programme—processing 700 sequenced genomes from Czech donors to analyse population-specific characteristics of variants.

The project hit hard limits: traditional tooling could not handle the data volume; there was no efficient way to store and query the dataset; and delivering an in-house solution would have required unsustainable compute and headcount.

02 —

The Reaction

Approach

DNAi deployed Floxgen Aggregation, which automates genomic processing and makes results analyst-ready without bespoke data engineering for every release.

Raw genetics are transformed into curated outputs; scientists can iterate when new samples arrive or the analysed cohort changes. One-click recalculation keeps downstream statistics aligned.

Technology

VCF ingestion and validation
Large-scale processing with Apache Hail
Indexing and search via ElasticSearch
Clinical-style variant annotation
Aggregation and statistical summaries
Access through GraphQL, relational stores, or ElasticSearch APIs
Web portal for exploratory analysis

03 —

The Effect

Outcomes

Up to about 90% shorter database build time versus prior manual approaches
Significant reduction in total cost to stand up the population resource
Removal of bespoke infrastructure and staffing bottlenecks

The programme enabled Czech Genome Portal as the reference environment for Czech researchers and clinicians, supporting precision medicine use cases.

Note: Repo folder / export slug is zpracovani-a-analyza-genomickych-dat-imtm; this CMS slug is different because Webflow still reports that base slug as taken without an exposed item row. Legacy Simplifying Genetic Research (index 1) stays unchanged.

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