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    21 repositories

    • genomics-status

      Public
      Tornado server for tracking samples at NGI Stockholm
      JavaScript
      •
      MIT License
      •18•12•0•2•Updated Mar 7, 2025Mar 7, 2025

    • ngisweden.se

      Public
      Wordpress theme and plugins for https://ngisweden.se
      PHP
      •
      MIT License
      •9•0•1•1•Updated Mar 5, 2025Mar 5, 2025

    • ngi_reports

      Public
      Code to generate reports for use by the NGI in SciLifeLab
      HTML
      •
      MIT License
      •13•5•0•0•Updated Mar 4, 2025Mar 4, 2025

    • anglerfish

      Public
      Anglerfish - Nanopore reads from Illumina libraries
      nanoporedemultiplexing
      Python
      •
      MIT License
      •4•2•15•1•Updated Feb 18, 2025Feb 18, 2025

    • standalone_scripts

      Public
      Repository to store standalone scripts that do not belong to any bigger package or repository
      Python
      •
      MIT License
      •22•5•0•1•Updated Feb 17, 2025Feb 17, 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
      •1•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • miarka-provision

      Public
      Ansible playbooks for provisioning NGI cluster Miarka
      Jinja
      •12•2•3•1•Updated Mar 4, 2025Mar 4, 2025

    • MultiQC_NGI

      Public
      MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
      Python
      •
      MIT License
      •9•3•0•0•Updated Jan 27, 2025Jan 27, 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

    • DailyRead

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

    • 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

    • 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

    • irma-provision

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

    • MosquitoRobots

      Public
      Protocols and plates with plate definitions for SPT Mosquito robots
      1•0•0•0•Updated Aug 31, 2021Aug 31, 2021

    • Loop-Genomics-Fusions

      Public
      R
      •1•0•0•0•Updated Feb 3, 2021Feb 3, 2021

    • icing

      Public
      An attempt to make HLA typing from OxfordNanopore reads (MinION platform)
      Python
      •
      MIT License
      •1•13•1•0•Updated Aug 20, 2018Aug 20, 2018

    • HTT-repeat-analysis

      Public
      R
      •1•0•1•0•Updated Aug 6, 2018Aug 6, 2018

    • internal-provisioning

      Public
      Ansible repository for deployment stuff
      Python
      •4•3•2•0•Updated Jun 1, 2018Jun 1, 2018

    • CAVA

      Public
      Count-based analysis of variants in long amplicons
      0•2•0•0•Updated Nov 10, 2017Nov 10, 2017

    • aliceflow

      Public
      NextFlow framework to streamline the Genalice variant call pipeline
      Groovy
      •2•2•2•0•Updated Sep 27, 2017Sep 27, 2017