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:

https://github.com/SciLifeLab https://github.com/NationalGenomicsInfrastructure

Highlighted projects

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

ewels/MultiQC

https://github.com/ewels/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report. - http://multiqc.info

nf-core/sarek

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

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing - https://nf-co.re/sarek

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/

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 https://nf-co.re/ 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