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
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:
Aggregate results from bioinformatics analyses across many samples into a single report. - http://multiqc.info
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing - https://nf-co.re/sarek
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria - http://checkqc.readthedocs.io/
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
Last Updated: 7th September 2022