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    85 repositories

    • iskylims

      Public
      is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics a…
      workflowlimsngs
      workflowlimsngsbioinformatics-analysisngs-analysisngs-data
      Python
      •
      GNU General Public License v3.0
      •43•95•18•5•Updated Aug 28, 2026Aug 28, 2026

    • relecov-platform

      Public
      genomic surveillance web platform for respiratory viruses used by RELECOV network in Spain
      bioinformaticssurveillanceinteroperability
      bioinformaticssurveillanceinteroperabilitydata-sharingfair-datacovid-19
      Python
      •
      GNU General Public License v3.0
      •11•1•3•4•Updated Aug 28, 2026Aug 28, 2026

    • pathocore-api

      Public
      Core API for managing and serving data for pathogen platforms and related services.
      Python
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Aug 28, 2026Aug 28, 2026

    • mepram-omop-api

      Public
      Core API for managing and serving data for the OMOP dashboard for the MEPRAM project.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Aug 28, 2026Aug 28, 2026

    • buisciii-tools

      Public
      set of helper tools for bu-isciii management of its core services portfolio.
      portfolioservicesbioinformatics
      portfolioservicesbioinformaticsgenomicscore-servicesbioinformatics-analysis
      Python
      •
      GNU General Public License v3.0
      •19•4•11•2•Updated Aug 28, 2026Aug 28, 2026

    • buisciii-deployment-standards

      Public
      Shell
      •1•0•1•0•Updated Aug 27, 2026Aug 27, 2026

    • viralrecon

      Public
      Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      •
      MIT License
      •157•1•0•0•Updated Aug 27, 2026Aug 27, 2026

    • relecov_2026_drylab_eqa

      Public
      Scripts to process the results from the 2026 RELECOV DryLab EQA
      Python
      •
      GNU General Public License v3.0
      •1•0•0•1•Updated Aug 26, 2026Aug 26, 2026

    • relecov-tools

      Public
      set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download…
      bioinformaticsgenomicssurveillance
      bioinformaticsgenomicssurveillancecovid-19sars-cov-2
      HTML
      •
      GNU General Public License v3.0
      •27•7•27•3•Updated Aug 25, 2026Aug 25, 2026

    • bd-tools

      Public
      Tools to process MePRAM data for ML
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Aug 21, 2026Aug 21, 2026

    • BU-ISCIII

      Public
      Our Wiki and main public documentation repository.
      documentationbioinformaticsbioinformatics-unit
      documentationbioinformaticsbioinformatics-unit
      11•7•3•0•Updated Aug 11, 2026Aug 11, 2026

    • pathocore-web

      Public
      TypeScript
      •2•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • LocalEGA

      Public
      A federated storage for sensitive data
      Python
      •
      Apache License 2.0
      •22•0•0•1•Updated Jul 29, 2026Jul 29, 2026

    • impact-tools

      Public
      Set of tools for pre-processing and ingestion of WGS Go-IMPaCT data into EGA and AF Beacon
      MIT License
      •2•0•0•0•Updated Jul 29, 2026Jul 29, 2026

    • beacon2-pi-api

      Public
      Beacon v2 Production Implementation (API)
      Python
      •
      Apache License 2.0
      •17•0•0•1•Updated Jul 28, 2026Jul 28, 2026

    • beacon2-ri-tools-v2

      Public
      Python
      •
      Apache License 2.0
      •17•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • OmicsExplorer

      Public
      Sandra Sanchez Pinilla TFM
      R
      •1•0•0•0•Updated May 12, 2026May 12, 2026

    • virology_training

      Public
      This repo contains all the resources needed to follow the virology training to analyze viral sequencing data.
      HTML
      •5•4•0•0•Updated Mar 26, 2026Mar 26, 2026

    • infectious-diseases-toolkit

      Public
      Infectious diseases toolkit
      Python
      •
      Other
      •46•1•0•0•Updated Mar 5, 2026Mar 5, 2026

    • flu_resistance

      Public
      Repository containing influenza resistance data in JSON format and scripts to generate and update these files from source datasets.
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Dec 15, 2025Dec 15, 2025

    • nexstrain_relecov

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • galaxy_virologist_training

      Public
      Galaxy training for virology profiles
      HTML
      •4•0•2•0•Updated Nov 5, 2025Nov 5, 2025

    • pdn_priority_pathogens

      Public
      Python
      •
      MIT License
      •4•1•0•0•Updated Oct 14, 2025Oct 14, 2025

    • introduction_to_hpc

      Public
      In this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.
      HTML
      •
      GNU General Public License v3.0
      •4•1•0•0•Updated Oct 3, 2025Oct 3, 2025

    • spanish-pathogens-portal

      Public
      A minimal/example hugo site for node pathogens portal. Checkout the demo site following the URL below
      HTML
      •
      MIT License
      •7•0•1•0•Updated Jun 26, 2025Jun 26, 2025

    • introduction_to_bioinformatics

      Public
      In this training course you will find theory and practice material for introducing yourself to the basics of high throughput sequencing data analysis.
      GNU General Public License v3.0
      •7•4•2•0•Updated Jun 12, 2025Jun 12, 2025

    • pikavirus

      Public
      New pikavirus in dsl2
      Nextflow
      •
      MIT License
      •6•2•5•0•Updated Mar 26, 2025Mar 26, 2025

    • PikaVirus_OLD

      Public
      Python
      •
      MIT License
      •3•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • taranys

      Public
      cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
      sequencingmlstcgmlst
      sequencingmlstcgmlstoutbreak-detectionbacterial-genomeswgmlstoutbreak-data-analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•9•3•0•Updated Jan 3, 2025Jan 3, 2025

    • rnaseq_nis_paper

      Public
      This repository contains custom R scripts for performing RNA-seq differential gene expression analysis, along with scripts for generating PCA plots and boxplots…
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
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