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    56 repositories

    • ngisweden.se-publications

      Public
      A GitHub action to fetch a random selection of publications to display on the website
      HTML
      •
      MIT License
      •0•0•0•8•Updated May 4, 2026May 4, 2026

    • dmx

      Public
      Helper scripts for demultiplexing
      Python
      •
      MIT License
      •3•0•0•0•Updated May 4, 2026May 4, 2026

    • miarka-provision

      Public
      Ansible playbooks for provisioning NGI cluster Miarka
      Jinja
      •16•2•6•0•Updated Apr 30, 2026Apr 30, 2026

    • genomics-status

      Public
      Tornado server for tracking samples at NGI Stockholm
      JavaScript
      •
      MIT License
      •21•12•0•5•Updated Apr 29, 2026Apr 29, 2026

    • MultiQC_NGI

      Public
      MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
      Python
      •
      MIT License
      •11•4•0•0•Updated Apr 29, 2026Apr 29, 2026

    • 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 Apr 29, 2026Apr 29, 2026

    • taca-ngi-pipeline

      Public
      A TACA plugin adding functionality relevant for the ngi_pipeline
      Python
      •
      MIT License
      •14•3•1•0•Updated Apr 28, 2026Apr 28, 2026

    • ngisweden.se

      Public
      Wordpress theme and plugins for https://ngisweden.se
      PHP
      •
      MIT License
      •9•0•1•0•Updated Apr 27, 2026Apr 27, 2026

    • ngi_reports

      Public
      Code to generate reports for use by the NGI in SciLifeLab
      Python
      •
      MIT License
      •14•5•0•0•Updated Apr 27, 2026Apr 27, 2026

    • dataflow_transfer

      Public
      Tool for transferring data from NAS to HPC
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • Yggdrasil

      Public
      Automate anything - traceable plans, reproducible runs.
      automationorchestrationevent-driven
      automationorchestrationevent-driven
      Python
      •
      MIT License
      •3•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • 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
      •865•0•0•2•Updated Apr 23, 2026Apr 23, 2026

    • ngi-firn

      Public
      A laboratory freezer inventory management system created with Nuxt4, Vue and UnaUI.
      Vue
      •
      MIT License
      •2•2•0•0•Updated Apr 21, 2026Apr 21, 2026

    • NGI_dashboards

      Public
      SciLifeLab NGI Dashboard Code
      dashboardkpi-targetsscilifelab
      dashboardkpi-targetsscilifelabnational-genomics-infrastructure
      HTML
      •
      MIT License
      •7•1•7•0•Updated Apr 21, 2026Apr 21, 2026

    • anglerfish

      Public
      Anglerfish - Nanopore reads from Illumina libraries
      nanoporedemultiplexing
      nanoporedemultiplexing
      Python
      •
      MIT License
      •5•6•17•2•Updated Apr 13, 2026Apr 13, 2026

    • scilifelab_epps

      Public
      A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
      Python
      •16•6•0•4•Updated Apr 8, 2026Apr 8, 2026

    • dataflow_archive

      Public
      Python
      •
      MIT License
      •1•0•0•1•Updated Mar 11, 2026Mar 11, 2026

    • StatusDB_seed_data

      Public
      Holds test data to fire up a dev instance of statusdb
      Shell
      •
      MIT License
      •2•0•0•1•Updated Mar 11, 2026Mar 11, 2026

    • LIMS2DB

      Public
      Python
      •
      MIT License
      •13•1•0•0•Updated Mar 2, 2026Mar 2, 2026

    • NGI_Element_benchmark

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • checklists_generator

      Public
      Python script to dynamically generate the bioinfo production checklists for QC, Delivery and Close of NGI sequencing projects
      Python
      •
      MIT License
      •2•2•0•0•Updated Feb 17, 2026Feb 17, 2026

    • ngi-landing

      Public
      Prototype of a possible new static NGI landing page built with Nuxt.
      Vue
      •1•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • 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 Jan 15, 2026Jan 15, 2026

    • irma-provision

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

    • radQC

      Public
      Pipeline for QC of RAD-seq data
      Nextflow
      •
      MIT License
      •1•5•2•0•Updated Oct 22, 2025Oct 22, 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
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