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    43 repositories

    • genomics-status

      Public
      Tornado server for tracking samples at NGI Stockholm
      JavaScript
      •
      MIT License
      •18•12•0•1•Updated Jan 10, 2025Jan 10, 2025

    • miarka-provision

      Public
      Ansible playbooks for provisioning NGI cluster Miarka
      Jinja
      •12•2•4•3•Updated Jan 9, 2025Jan 9, 2025

    • scilifelab_epps

      Public
      A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
      Python
      •14•5•0•1•Updated Jan 9, 2025Jan 9, 2025

    • ngi_pipeline

      Public
      Code driving the production pipeline at SciLifeLab
      Python
      •25•6•22•0•Updated Jan 9, 2025Jan 9, 2025

    • 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 Jan 9, 2025Jan 9, 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 Jan 9, 2025Jan 9, 2025

    • taca-ngi-pipeline

      Public
      A TACA plugin adding functionality relevant for the ngi_pipeline
      Python
      •
      MIT License
      •14•3•1•1•Updated Jan 9, 2025Jan 9, 2025

    • ngi_reports

      Public
      Code to generate reports for use by the NGI in SciLifeLab
      HTML
      •
      MIT License
      •13•5•0•1•Updated Jan 9, 2025Jan 9, 2025

    • LIMS2DB

      Public
      Python
      •
      MIT License
      •12•1•0•1•Updated Jan 9, 2025Jan 9, 2025

    • DailyRead

      Public
      The NGI Daily Read
      Python
      •2•0•2•1•Updated Jan 9, 2025Jan 9, 2025

    • MultiQC_NGI

      Public
      MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
      Python
      •
      MIT License
      •9•3•0•0•Updated Jan 9, 2025Jan 9, 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
      •716•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • nfcore_sarek

      Public
      NGI fork of the original nf-core/sarek pipeline. May have minor bugfixes for running the pipeline on the NGI used HPC.
      Nextflow
      •
      MIT License
      •420•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • TACA

      Public
      Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
      Python
      •
      MIT License
      •19•14•13•2•Updated Dec 16, 2024Dec 16, 2024

    • 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
      •1•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • NGI_dashboards

      Public
      SciLifeLab NGI Dashboard Code
      dashboardkpi-targetsscilifelabnational-genomics-infrastructure
      HTML
      •
      MIT License
      •7•1•7•0•Updated Oct 10, 2024Oct 10, 2024

    • lims_dashboard

      Public
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 5, 2024Oct 5, 2024

    • ngisweden.se

      Public
      Wordpress theme and plugins for https://ngisweden.se
      PHP
      •
      MIT License
      •9•0•1•1•Updated Oct 1, 2024Oct 1, 2024

    • anglerfish

      Public
      Anglerfish - Nanopore reads from Illumina libraries
      nanoporedemultiplexing
      Python
      •
      MIT License
      •4•2•15•1•Updated Aug 19, 2024Aug 19, 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

    • genologics_sql

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

    • 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 Jul 3, 2024Jul 3, 2024

    • 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 Jul 2, 2024Jul 2, 2024

    • tower-showcase

      Public
      Infrastructure as code implementation of the seqeralabs/showcase Workspace in Tower Cloud
      Shell
      •
      Mozilla Public License 2.0
      •11•0•0•0•Updated May 6, 2024May 6, 2024

    • NGI-AS-tech_note-2024

      Public
      MIT License
      •1•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • spectacles

      Public
      API for a clearer look at clarity
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • umi-injector

      Public
      umi-injector integrates UMI sequences from a separate FastQ file into the read headers of a single or paired FastQ.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Apr 12, 2023Apr 12, 2023

    • mdx_outline

      Public
      Python-Markdown extension to wrap the document logical sections (as implied by h1-h6 headings)
      Python
      •
      Other
      •19•0•0•0•Updated Aug 26, 2022Aug 26, 2022

    • OrderPortal

      Public
      A portal for orders (requests, project applications, etc) to a facility from its users.
      Python
      •
      MIT License
      •12•0•0•0•Updated Aug 4, 2022Aug 4, 2022

    • irma-provision

      Public
      Ansible playbooks for provisioning NGI pipeline and related sw
      Jinja
      •17•1•9•0•Updated Mar 3, 2022Mar 3, 2022