Skip to content

@genomic-medicine-sweden Genomic Medicine Sweden

Change the repository type filter

All

    Repositories list

    36 repositories

    • nallo

      Public
      An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
      nanoporepacbiogmsvariant-callinglong-read-sequencing
      Nextflow
      •
      MIT License
      •4•17•93•1•Updated Oct 30, 2024Oct 30, 2024

    • raredisease

      Public
      Call and score variants from WGS/WES of rare disease patients.
      Nextflow
      •
      MIT License
      •34•1•0•0•Updated Oct 30, 2024Oct 30, 2024

    • Twist_Solid

      Public
      Pipeline for Solid tumours
      Python
      •
      GNU General Public License v3.0
      •6•3•22•7•Updated Oct 30, 2024Oct 30, 2024

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •351•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • tomte

      Public
      A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient
      Nextflow
      •
      MIT License
      •3•12•9•0•Updated Oct 29, 2024Oct 29, 2024

    • jasen

      Public
      Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
      pipelinetypingclinicalresistancemicrobial
      Nextflow
      •
      GNU General Public License v3.0
      •11•9•39•1•Updated Oct 28, 2024Oct 28, 2024

    • gms_16S

      Public
      A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
      Groovy
      •
      GNU General Public License v3.0
      •1•6•14•1•Updated Oct 28, 2024Oct 28, 2024

    • meta-val

      Public
      nf-core/taxprofiler post-processing; verification of classification results; consensus maps
      Nextflow
      •
      MIT License
      •2•3•4•1•Updated Oct 24, 2024Oct 24, 2024

    • MIMOSA

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • meta-vis

      Public
      Visualisation of metagenomic analysis results
      Python
      •0•1•20•2•Updated Oct 21, 2024Oct 21, 2024

    • gms-artic

      Public
      A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
      Nextflow
      •
      GNU Affero General Public License v3.0
      •89•9•14•3•Updated Oct 18, 2024Oct 18, 2024

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •713•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • taxprofiler

      Public
      Taxonomic profiling of shotgun metagenomic data
      Nextflow
      •
      MIT License
      •34•0•18•0•Updated Oct 11, 2024Oct 11, 2024

    • NGPIris

      Public
      NGPIris 👁 (intelligence and repository interface software) is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform
      Python
      •
      GNU General Public License v2.0
      •3•0•15•1•Updated Oct 2, 2024Oct 2, 2024

    • Twist_Solid_pipeline_files

      Public
      Design and filter files used by the pipeline
      0•1•1•0•Updated Sep 24, 2024Sep 24, 2024

    • poppy

      Public
      Python
      •
      GNU General Public License v3.0
      •2•3•3•2•Updated Sep 20, 2024Sep 20, 2024

    • .github

      Public
      0•0•0•0•Updated Aug 15, 2024Aug 15, 2024

    • MultiQC

      Public
      Aggregate results from bioinformatics analyses across many samples into a single report.
      JavaScript
      •
      GNU General Public License v3.0
      •601•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • pgx

      Public
      Pharmacogenomics pipeline
      HTML
      •
      GNU General Public License v3.0
      •2•8•4•1•Updated Jul 1, 2024Jul 1, 2024

    • NGPGlue

      Public archive
      Small scripts and other similar NGP solutions of sensitive nature
      Perl
      •
      GNU General Public License v2.0
      •0•0•3•0•Updated May 15, 2024May 15, 2024

    • RareDisease_RNA_workflow

      Public archive
      Nextflow
      •5•2•3•2•Updated Apr 18, 2024Apr 18, 2024

    • gmsmetapost

      Public archive
      GMS Metagenomics post-classification
      Nextflow
      •
      MIT License
      •1•0•13•1•Updated Apr 18, 2024Apr 18, 2024

    • validate-meta

      Public archive
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 18, 2024Apr 18, 2024

    • micro-site-data-sharing

      Public archive
      This repo shares data between sites for the development of GMS-micro solutions.
      MIT License
      •2•1•0•0•Updated Apr 18, 2024Apr 18, 2024

    • GMS_RD_LR

      Public
      GMS Best practises for long read analysis
      0•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • Information-specifications

      Public
      GNU General Public License v3.0
      •1•3•1•0•Updated Jan 22, 2024Jan 22, 2024

    • microbiology

      Public
      A repo to collect information about all different projects we have in GMS-Micro
      0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • docker-sc2reporter

      Public
      Dockerized version of the sc2reporter program.
      JavaScript
      •
      GNU General Public License v2.0
      •1•0•24•0•Updated Oct 26, 2023Oct 26, 2023

    • nextflow-modules

      Public
      Shared nextflow modules and assets
      Perl
      •
      GNU General Public License v3.0
      •2•0•0•1•Updated Apr 24, 2023Apr 24, 2023

    • taxpasta

      Public
      TAXnomic Profile Aggregation and STAndardisation
      Python
      •
      Apache License 2.0
      •7•1•0•0•Updated Mar 6, 2023Mar 6, 2023