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    78 repositories

    • bd-tools

      Public
      Tools to process MePRAM data for ML
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Apr 29, 2026Apr 29, 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•15•1•Updated Apr 29, 2026Apr 29, 2026

    • viralrecon

      Public
      Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      •
      MIT License
      •148•1•0•0•Updated Apr 28, 2026Apr 28, 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•0•Updated Apr 22, 2026Apr 22, 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•18•4•Updated Apr 16, 2026Apr 16, 2026

    • 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
      •41•91•16•3•Updated Apr 16, 2026Apr 16, 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

    • 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
      •29•7•30•4•Updated Mar 25, 2026Mar 25, 2026

    • infectious-diseases-toolkit

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

    • BU-ISCIII

      Public
      Our Wiki and main public documentation repository.
      documentationbioinformaticsbioinformatics-unit
      documentationbioinformaticsbioinformatics-unit
      11•7•5•0•Updated Feb 19, 2026Feb 19, 2026

    • beacon2-pi-api

      Public
      Beacon v2 Production Implementation (API)
      Python
      •
      Apache License 2.0
      •14•0•0•0•Updated Jan 27, 2026Jan 27, 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

    • LocalEGA

      Public
      A federated storage for sensitive data
      Python
      •
      Apache License 2.0
      •22•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • galaxy_virologist_training

      Public
      Galaxy training for virology profiles
      HTML
      •5•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
      •3•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
      •7•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
      •5•9•0•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

    • bacass

      Public
      Simple bacterial assembly and annotation pipeline
      Nextflow
      •
      MIT License
      •69•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • bacterial_wgs_training

      Public
      In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
      genomenextflowsequencing
      genomenextflowsequencingwgsngs-analysisoutbreak-detectionbacterial-genomesoutbreaksbacterial-wgs-trainingwgs-analysis
      HTML
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Oct 31, 2024Oct 31, 2024

    • buisciii.github.io

      Public
      BU-ISCIII team website
      SCSS
      •
      MIT License
      •2.7k•0•0•0•Updated May 20, 2024May 20, 2024

    • MPXstreveal

      Public
      Monkepox STR reveal (MPXstreveal) a new draft approach for detecting and curating low complexity regions in monkeypox genomes using massive parallel sequencing.
      Python
      •
      MIT License
      •2•3•0•0•Updated Feb 28, 2024Feb 28, 2024

    • eutils_search_cd44_paper

      Public
      This repository contains a custom python script that finds citations that include the name of a gene along with a condition provided by the user. P.e brca2+AND+…
      Python
      •
      MIT License
      •1•0•0•0•Updated May 26, 2023May 26, 2023

    • cna_bacterial_wgs_training

      Public
      In this training course you will find theory and practice material for introducing yourself to wgs analysis for foodborne bacteria
      2•0•0•0•Updated Nov 8, 2022Nov 8, 2022

    • assemblybacterias

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Sep 26, 2022Sep 26, 2022
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