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).

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

Highlighted projects

Here are a few highlights of free and open-source software that has either been created by NGI staff or to which we contributed greatly:

nf-core/sarek

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing - https://nf-co.re/sarek

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Molmed/checkQC

https://github.com/Molmed/checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria - http://checkqc.readthedocs.io/

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nf-core/seqinspector

https://github.com/nf-core/seqinspector

Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput. - https://nf-co.re/seqinspector

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nf-core/references

https://github.com/nf-core/references

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases - https://nf-co.re/references

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Analysis pipelines with nf-core

The NGI has authored a number of bioinformatics analysis pipelines for different data types, some of which are featured in the Highlighted Projects above. The nf-core community was founded to collect and standardise these pipelines, collaborate on their maintenance and improvement, and make them available to other genomics cores and research groups. Because several nf-core pipelines were conceived at NGI and we contributed to many others, you can find a small trace of NGI in much of the nf-core ecosystem.

nf-core/rnaseq

https://github.com/nf-core/rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - https://nf-co.re/rnaseq

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nf-core/tools

https://github.com/nf-core/tools

Python package with helper tools for the nf-core community. - https://nf-co.re

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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/Apptainer, 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. We are proud supporters of the collaborative, international community that nf-core is today. The community is a prime example of the power of free and open-source software, uniting an ever-growing number of contributors and users from all over the world. For more information, see https://nf-co.re/ or the nf-core publications:

Last Updated: 27th January 2026