Skip to content

@SciLifeLab Science For Life Laboratory

Change the repository type filter

All

    Repositories list

    47 repositories

    • TIDDIT

      Public
      TIDDIT - structural variant calling
      Cython
      •
      Other
      •17•78•5•0•Updated Mar 22, 2026Mar 22, 2026

    • umi-transfer

      Public
      A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.
      Rust
      •
      MIT License
      •1•6•1•0•Updated Feb 27, 2026Feb 27, 2026

    • architecture

      Public
      Technical architecture governance for SciLifeLab infrastructure - ensuring interoperability, standards, and sustainable design
      Shell
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•2•1•Updated Dec 11, 2025Dec 11, 2025

    • genologics

      Public
      Python interface to the GenoLogics LIMS server via its REST API.
      Python
      •
      MIT License
      •54•30•9•0•Updated Aug 13, 2025Aug 13, 2025

    • facs

      Public
      Fast and Accurate Classification of Sequences using Bloom filters
      Jupyter Notebook
      •
      Other
      •9•16•8•0•Updated Apr 19, 2023Apr 19, 2023

    • OrderPortal

      Public
      A portal for orders (a.k.a. requests, project applications) to a SciLifeLab facility from its users.
      Python
      •
      MIT License
      •14•1•0•0•Updated Oct 18, 2022Oct 18, 2022

    • standalone_scripts-1

      Public archive
      Repository to store standalone scripts that do not belong to any bigger package or repository
      Python
      •
      MIT License
      •23•1•0•0•Updated Jun 20, 2022Jun 20, 2022

    • percolator

      Public
      Semi-supervised learning for peptide identification from shotgun proteomics datasets
      C++
      •
      Other
      •45•0•0•0•Updated Jan 5, 2021Jan 5, 2021

    • coronastatus

      Public
      Open source webapp that let people report their health status to get overview of COVID-19 🇳🇴🇳🇱🇸🇰🇲🇽🇮🇹🇮🇳🇵🇭🇸🇪🇩🇰🇹🇷🇧🇪
      HTML
      •
      MIT License
      •85•0•1•0•Updated Mar 28, 2020Mar 28, 2020

    • scilifelab

      Public archive
      Misc code snippets for Science For Life Laboratory
      Python
      •
      MIT License
      •25•5•10•0•Updated Jan 30, 2020Jan 30, 2020

    • Sarek

      Public archive
      Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
      dockerworkflowbioinformatics
      dockerworkflowbioinformaticspipelinegenomicsnextflowcancersomatic-variantsreproducible-researchcontainers
      Nextflow
      •
      MIT License
      •526•133•0•0•Updated Jan 27, 2020Jan 27, 2020

    • courses

      Public
      Course homepages for some of the courses given at SciLifeLab
      HTML
      •73•21•0•0•Updated Jan 23, 2020Jan 23, 2020

    • Sarek-data

      Public archive
      Sarek test data and references
      Python
      •
      MIT License
      •6•3•0•0•Updated May 14, 2019May 14, 2019

    • SVDB

      Public
      structural variant database software
      Python
      •21•2•0•0•Updated Mar 15, 2019Mar 15, 2019

    • NGI-NeutronStar

      Public archive
      De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.
      bioinformaticspipelinenextflow
      bioinformaticspipelinenextflowdenovo-assembly
      Nextflow
      •
      MIT License
      •7•2•0•0•Updated Oct 5, 2018Oct 5, 2018

    • NGI-RNAfusion

      Public archive
      RNA pipeline for fusion detection
      Groovy
      •
      MIT License
      •122•4•0•0•Updated Oct 5, 2018Oct 5, 2018

    • NGI-ChIPseq

      Public archive
      Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm
      bioinformaticspipelinenextflow
      bioinformaticspipelinenextflowbioinformatics-pipelinechip-seq
      Groovy
      •
      MIT License
      •176•7•0•0•Updated Aug 20, 2018Aug 20, 2018

    • NGI-RNAseq

      Public archive
      Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
      bioinformaticsrna-seqpipeline
      bioinformaticsrna-seqpipelinenextflowrnaseqrna-sequencing
      Groovy
      •
      MIT License
      •860•51•0•0•Updated Aug 20, 2018Aug 20, 2018

    • NGI-smRNAseq

      Public archive
      Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
      Groovy
      •
      MIT License
      •133•5•0•0•Updated Jul 12, 2018Jul 12, 2018

    • NGI-ExoSeq

      Public archive
      This pipeline has moved! Please see:
      nextflowbioinformatics-pipelineexome-pipeline
      nextflowbioinformatics-pipelineexome-pipelinebioinformatics-analysisexome-sequencing
      Groovy
      •
      MIT License
      •27•8•0•0•Updated Apr 18, 2018Apr 18, 2018

    • NouGAT

      Public
      NouGAT is a pipeline that automates de novo assembly project tasks, generating a first draft assembly.
      Python
      •
      MIT License
      •17•7•3•0•Updated Apr 10, 2018Apr 10, 2018

    • NGI-NextflowDocs

      Public archive
      Common documentation for National Genomics Infrastructure pipelines built with Nextflow
      Groovy
      •
      MIT License
      •4•5•1•0•Updated Mar 29, 2018Mar 29, 2018

    • NGI-MethylSeq

      Public archive
      This pipeline has moved! Please see:
      Groovy
      •
      MIT License
      •171•11•1•0•Updated Mar 12, 2018Mar 12, 2018

    • NGI-CellRaiser

      Public
      Pipeline for analysing 10X single cell data
      Groovy
      •
      MIT License
      •4•8•2•0•Updated Jan 23, 2018Jan 23, 2018

    • CAW-containers

      Public archive
      Containers for CAW
      dockerbioinformaticsnextflow
      dockerbioinformaticsnextflowcancercontainerssingularity
      2•3•0•0•Updated Nov 20, 2017Nov 20, 2017

    • joint_variant_calling

      Public
      Shell
      •3•0•0•0•Updated Mar 15, 2017Mar 15, 2017

    • hugin

      Public
      Status monitor
      Python
      •6•2•4•0•Updated Mar 3, 2016Mar 3, 2016

    • genomics-dashboard

      Public
      JavaScript
      •
      MIT License
      •2•3•3•0•Updated Jun 30, 2015Jun 30, 2015

    • external_kpis

      Public
      JavaScript
      •1•0•0•0•Updated Jun 30, 2015Jun 30, 2015

    • scilifelab_parsers

      Public
      Module for scilifelab parsers of metrics and other files
      Python
      •2•1•0•0•Updated Apr 13, 2015Apr 13, 2015
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.