nf-core is a community-driven initiative that provides a curated set of analysis workflows built using Nextflow. These workflows are designed to be scalable, reproducible, and standardised, ensuring high-quality bioinformatics analyses across different research domains. By fostering collaboration and best practices, nf-core helps streamline computational biology and genomics research.
GHGA collaborates with nf-core to develop, maintain and support the use of standardised bioinformatics workflows. Rather than creating new workflows independently, GHGA works with nf-core and other relevant communities to improve and adapt existing pipelines for genomic and phenotypic data processing. This ensures that GHGA’s workflows align with widely accepted community standards while remaining interoperable and efficient.
This collaboration helps to streamline our pipelines, avoid redundancy, enhances workflow sustainability, and supports a FAIR-compliant data analysis ecosystem. By integrating with nf-core, GHGA contributes to open science by improving workflow functionality and usability, making it easier for researchers to process genomic data in a secure and reproducible manner.
A recent publication with GHGA contribution introduces nf-core/sarek 3, a comprehensive variant calling and annotation pipeline designed for both germline and somatic samples.
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Benchmarking small pathogenic and structural variants can be challenging. Utilizing cutting-edge SeraSeq, GHGA partners with the NGS-CN to start a new initiative to benchmark NGS pipelines.
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GHGA joined the de.NBI/ELIXIR-Germany Spatial Hackathon ‘SpaceHack2.0’, advancing community-driven benchmarking.
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