NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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Open source code

Open source code is released under a licence that allows others to use that code for their own purposes. Releasing code in this way helps to foster transparency and co-operation within the academic society.

SciLifeLab open-source policy

The NGI takes open-source practices very seriously and was a founding member of the SciLifeLab open-source policy. All code we write is worked on openly on the code-sharing website GitHub. Where possible, projects are released as packages that can be used by others under an OSI-compliant licence (typically MIT).

All NGI code can be found at the following two GitHub organisations:

Highlighted projects

The SciLifeLab open-source portal lists active projects maintained at SciLifeLab, many of which have been developed at the NGI. Here are a few highlights:


Aggregate results from bioinformatics analyses across many samples into a single report. -


Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing -


CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria -

Analysis pipelines with nf-core

The NGI has authored a number of bioinformatics analysis pipelines for different data types. The nf-core community was founded to collect and standardise these, making them available to other genomics cores and research groups.

All nf-core pipelines are created using Nextflow: a computational analysis workflow framework and language. All nf-core pipelines bundle software using Conda, Docker or Singularity meaning that they can be run on virtually any computational infrastructure.

The NGI helps to lead the nf-core community, with several members in the core team. The community is made up of groups all over the world and an ever-growing number of contributors and users. For more information, see or the nf-core publication:

The nf-core framework for community-curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen

Nat Biotechnology (2020); doi: 10.1038/s41587-020-0439-x