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    57 repositories

    • scilifelab_epps

      Public
      A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
      Python
      •14•5•0•0•Updated Oct 2, 2024Oct 2, 2024

    • TACA

      Public
      Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
      Python
      •
      MIT License
      •19•13•13•1•Updated Sep 30, 2024Sep 30, 2024

    • genomics-status

      Public
      Tornado server for tracking samples at NGI Stockholm
      JavaScript
      •
      MIT License
      •18•12•0•3•Updated Sep 27, 2024Sep 27, 2024

    • standalone_scripts

      Public
      Repository to store standalone scripts that do not belong to any bigger package or repository
      Python
      •
      MIT License
      •23•4•0•1•Updated Sep 16, 2024Sep 16, 2024

    • LIMS2DB

      Public
      Python
      •
      MIT License
      •12•1•0•0•Updated Sep 12, 2024Sep 12, 2024

    • genologics

      Public
      Python interface to the GenoLogics LIMS server via its REST API.
      Python
      •
      MIT License
      •52•29•9•0•Updated Aug 26, 2024Aug 26, 2024

    • statusdb

      Public
      Python wrappers and methods to work with CouchDB's instance at NGI Stockholm
      Python
      •
      MIT License
      •9•2•0•0•Updated Aug 2, 2024Aug 2, 2024

    • TIDDIT

      Public
      TIDDIT - structural variant calling
      Cython
      •
      Other
      •13•67•8•0•Updated Jul 19, 2024Jul 19, 2024

    • genologics_sql

      Public
      Python interface for the Genologics Postgres database.
      Python
      •
      MIT License
      •9•1•0•0•Updated Jul 16, 2024Jul 16, 2024

    • 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
      •2•6•1•0•Updated Jul 2, 2024Jul 2, 2024

    • taca-ngi-pipeline

      Public
      A TACA plugin adding functionality relevant for the ngi_pipeline
      Python
      •
      MIT License
      •14•3•1•1•Updated Jul 2, 2024Jul 2, 2024

    • flowcell_parser

      Public
      Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output
      Python
      •
      MIT License
      •18•7•1•0•Updated Jan 22, 2024Jan 22, 2024

    • 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
      •12•1•0•0•Updated Oct 18, 2022Oct 18, 2022

    • standalone_scripts-1

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

    • percolator

      Public
      Semi-supervised learning for peptide identification from shotgun proteomics datasets
      C++
      •
      Other
      •36•0•0•0•Updated Jan 5, 2021Jan 5, 2021

    • bravo-protocols

      Public
      VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.
      JavaScript
      •
      Apache License 2.0
      •6•0•0•0•Updated Apr 2, 2020Apr 2, 2020

    • coronastatus

      Public
      Open source webapp that let people report their health status to get overview of COVID-19 🇳🇴🇳🇱🇸🇰🇲🇽🇮🇹🇮🇳🇵🇭🇸🇪🇩🇰🇹🇷🇧🇪
      HTML
      •
      MIT License
      •89•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
      dockerworkflowbioinformaticspipelinegenomicscancersomatic-variantsreproducible-researchcontainersnext-generation-sequencing
      Nextflow
      •
      MIT License
      •403•132•0•0•Updated Jan 27, 2020Jan 27, 2020

    • courses

      Public
      Course homepages for some of the courses given at SciLifeLab
      HTML
      •70•20•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
      •16•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.
      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
      •93•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
      bioinformaticsbioinformatics-pipelinechip-seqpipelinenextflow
      Groovy
      •
      MIT License
      •145•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-seqpipelinenextflowrnaseqrna-sequencing
      Groovy
      •
      MIT License
      •696•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
      •124•5•0•0•Updated Jul 12, 2018Jul 12, 2018

    • internal-provisioning

      Public
      Ansible repository for deployment stuff
      Python
      •3•3•2•0•Updated Jun 1, 2018Jun 1, 2018

    • NGI-ExoSeq

      Public archive
      This pipeline has moved! Please see:
      nextflowbioinformatics-pipelineexome-pipelinebioinformatics-analysisexome-sequencing
      Groovy
      •
      MIT License
      •28•8•0•0•Updated Apr 18, 2018Apr 18, 2018