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    54 repositories

    • ngisweden.se-publications

      Public
      A GitHub action to fetch a random selection of publications to display on the website
      TypeScript
      •
      MIT License
      •0•0•0•8•Updated Jan 5, 2026Jan 5, 2026

    • genomics-status

      Public
      Tornado server for tracking samples at NGI Stockholm
      JavaScript
      •
      MIT License
      •19•12•0•5•Updated Dec 23, 2025Dec 23, 2025

    • miarka-provision

      Public
      Ansible playbooks for provisioning NGI cluster Miarka
      Jinja
      •16•2•6•1•Updated Dec 22, 2025Dec 22, 2025

    • LIMS2DB

      Public
      Python
      •
      MIT License
      •13•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • ngi-firn

      Public
      A laboratory freezer inventory management system created with Nuxt4, Vue and UnaUI.
      Vue
      •
      MIT License
      •2•1•0•0•Updated Dec 18, 2025Dec 18, 2025

    • dataflow_transfer

      Public
      Tool for transferring data from NAS to HPC
      Python
      •2•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • nfcore_rnaseq

      Public
      NGI fork of the original nf-core/rnaseq pipeline. May have minor bugfixes for running the pipeline on the NGI used HPC.
      Nextflow
      •
      MIT License
      •830•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • scilifelab_epps

      Public
      A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
      Python
      •16•6•0•1•Updated Dec 17, 2025Dec 17, 2025

    • StatusDB_seed_data

      Public
      Holds test data to fire up a dev instance of statusdb
      Dockerfile
      •
      MIT License
      •2•0•0•1•Updated Dec 4, 2025Dec 4, 2025

    • TACA

      Public
      Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
      Python
      •
      MIT License
      •20•14•3•1•Updated Nov 28, 2025Nov 28, 2025

    • NGI_dashboards

      Public
      SciLifeLab NGI Dashboard Code
      dashboardkpi-targetsscilifelabnational-genomics-infrastructure
      HTML
      •
      MIT License
      •7•1•7•0•Updated Nov 27, 2025Nov 27, 2025

    • dmx

      Public
      Helper scripts for demultiplexing
      Python
      •
      MIT License
      •3•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • Yggdrasil

      Public
      Yggrasil is middleware platform designed to aggregate sample-related metadata, manage the execution of various pipelines for processing sequencing data, and ultimately handle the delivery of analyzed data.
      Python
      •
      MIT License
      •3•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • irma-provision

      Public archive
      Ansible playbooks for provisioning NGI pipeline and related sw
      Jinja
      •17•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • standalone_scripts

      Public
      Repository to store standalone scripts that do not belong to any bigger package or repository
      Python
      •
      MIT License
      •23•5•0•1•Updated Nov 18, 2025Nov 18, 2025

    • MultiQC_NGI

      Public
      MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
      Python
      •
      MIT License
      •11•4•0•2•Updated Nov 10, 2025Nov 10, 2025

    • ngi_pipeline

      Public
      Code driving the production pipeline at SciLifeLab
      Python
      •26•7•22•0•Updated Nov 10, 2025Nov 10, 2025

    • DailyRead

      Public
      The NGI Daily Read
      Python
      •2•0•2•0•Updated Nov 6, 2025Nov 6, 2025

    • flowcell_parser

      Public
      Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output
      Python
      •
      MIT License
      •18•7•1•0•Updated Nov 5, 2025Nov 5, 2025

    • lims_dashboard

      Public
      Python
      •
      MIT License
      •6•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • ngi_reports

      Public
      Code to generate reports for use by the NGI in SciLifeLab
      Python
      •
      MIT License
      •14•5•0•1•Updated Oct 29, 2025Oct 29, 2025

    • radQC

      Public
      Pipeline for QC of RAD-seq data
      Nextflow
      •
      MIT License
      •1•4•2•0•Updated Oct 22, 2025Oct 22, 2025

    • NGI_Element_benchmark

      Public
      HTML
      •1•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • NGI_scWGS_technote_2025

      Public
      Filtes related benchmarking scWGS kits at NGI Stockholm 2025
      HTML
      •1•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • charon

      Public
      Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.
      Python
      •
      MIT License
      •10•3•4•0•Updated Oct 7, 2025Oct 7, 2025

    • userman

      Public
      Simple user account handling system for use with web services. Built on top of Tornado and CouchDb.
      Python
      •
      MIT License
      •3•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • genologics_sql

      Public
      Python interface for the Genologics Postgres database.
      Python
      •
      MIT License
      •9•1•0•0•Updated Sep 30, 2025Sep 30, 2025

    • NGI-ONT_scRNAseq-tech_note-2025

      Public
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • taca-ngi-pipeline

      Public
      A TACA plugin adding functionality relevant for the ngi_pipeline
      Python
      •
      MIT License
      •14•3•1•0•Updated Aug 13, 2025Aug 13, 2025

    • ngisweden.se

      Public
      Wordpress theme and plugins for https://ngisweden.se
      PHP
      •
      MIT License
      •9•0•1•0•Updated Jun 10, 2025Jun 10, 2025