Repositories list

• 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

  •44 forks in BU-ISCIII/introduction_to_hpc•33 stars in BU-ISCIII/introduction_to_hpc•00 issues in BU-ISCIII/introduction_to_hpc•00 pull requests in BU-ISCIII/introduction_to_hpc•Updated Oct 16, 2026Oct 16, 2026

• buisciii-tools

  Public
  set of helper tools for bu-isciii management of its core services portfolio.

  portfolioservicesbioinformatics+ 3

  portfolioservicesbioinformaticsgenomicscore-servicesbioinformatics-analysis

  Python

  •

  GNU General Public License v3.0

  •1919 forks in BU-ISCIII/buisciii-tools•44 stars in BU-ISCIII/buisciii-tools•1111 issues in BU-ISCIII/buisciii-tools•11 pull request in BU-ISCIII/buisciii-tools•Updated Oct 16, 2026Oct 16, 2026

• viralrecon

  Public
  Assembly and intrahost/low-frequency variant calling for viral samples

  Nextflow

  •

  MIT License

  •158158 forks in BU-ISCIII/viralrecon•11 star in BU-ISCIII/viralrecon•00 issues in BU-ISCIII/viralrecon•00 pull requests in BU-ISCIII/viralrecon•Updated Oct 16, 2026Oct 16, 2026

• mepram-omop-api

  Public
  Core API for managing and serving data for the OMOP dashboard for the MEPRAM project.

  Shell

  •

  GNU General Public License v3.0

  •22 forks in BU-ISCIII/mepram-omop-api•00 stars in BU-ISCIII/mepram-omop-api•00 issues in BU-ISCIII/mepram-omop-api•00 pull requests in BU-ISCIII/mepram-omop-api•Updated Oct 16, 2026Oct 16, 2026

• beacon2-pi-api

  Public
  Beacon v2 Production Implementation (API)

  Python

  •

  Apache License 2.0

  •1818 forks in BU-ISCIII/beacon2-pi-api•00 stars in BU-ISCIII/beacon2-pi-api•00 issues in BU-ISCIII/beacon2-pi-api•00 pull requests in BU-ISCIII/beacon2-pi-api•Updated Oct 15, 2026Oct 15, 2026

• buisciii-deployment-standards

  Public
  BU-ISCIII deployment standards, reusable templates, and tooling for consistent containerized application deployments with Docker and Podman.

  dockerdeploymentvirtual-machine+ 1

  dockerdeploymentvirtual-machinepodman

  Shell

  •33 forks in BU-ISCIII/buisciii-deployment-standards•00 stars in BU-ISCIII/buisciii-deployment-standards•33 issues in BU-ISCIII/buisciii-deployment-standards•00 pull requests in BU-ISCIII/buisciii-deployment-standards•Updated Oct 15, 2026Oct 15, 2026

• impact-tools

  Public
  Set of tools for pre-processing and ingestion of WGS Go-IMPaCT data into EGA and AF Beacon

  MIT License

  •22 forks in BU-ISCIII/impact-tools•00 stars in BU-ISCIII/impact-tools•00 issues in BU-ISCIII/impact-tools•00 pull requests in BU-ISCIII/impact-tools•Updated Oct 14, 2026Oct 14, 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+ 3

  workflowlimsngsbioinformatics-analysisngs-analysisngs-data

  Python

  •

  GNU General Public License v3.0

  •4444 forks in BU-ISCIII/iskylims•9696 stars in BU-ISCIII/iskylims•1818 issues in BU-ISCIII/iskylims•00 pull requests in BU-ISCIII/iskylims•Updated Oct 13, 2026Oct 13, 2026

• relecov-platform

  Public
  genomic surveillance web platform for respiratory viruses used by RELECOV network in Spain

  bioinformaticssurveillanceinteroperability+ 3

  bioinformaticssurveillanceinteroperabilitydata-sharingfair-datacovid-19

  Python

  •

  GNU General Public License v3.0

  •1111 forks in BU-ISCIII/relecov-platform•11 star in BU-ISCIII/relecov-platform•33 issues in BU-ISCIII/relecov-platform•33 pull requests in BU-ISCIII/relecov-platform•Updated Oct 8, 2026Oct 8, 2026

• BU-ISCIII

  Public
  Our Wiki and main public documentation repository.

  documentationbioinformaticsbioinformatics-unit

  documentationbioinformaticsbioinformatics-unit

  1111 forks in BU-ISCIII/BU-ISCIII•77 stars in BU-ISCIII/BU-ISCIII•44 issues in BU-ISCIII/BU-ISCIII•00 pull requests in BU-ISCIII/BU-ISCIII•Updated Sep 29, 2026Sep 29, 2026

• LocalEGA

  Public
  A federated storage for sensitive data

  Python

  •

  Apache License 2.0

  •2323 forks in BU-ISCIII/LocalEGA•00 stars in BU-ISCIII/LocalEGA•00 issues in BU-ISCIII/LocalEGA•00 pull requests in BU-ISCIII/LocalEGA•Updated Sep 29, 2026Sep 29, 2026

• SNPhylo

  Public
  A pipeline to generate a phylogenetic tree from huge SNP data

  Shell

  •

  GNU General Public License v2.0

  •3838 forks in BU-ISCIII/SNPhylo•00 stars in BU-ISCIII/SNPhylo•00 issues in BU-ISCIII/SNPhylo•00 pull requests in BU-ISCIII/SNPhylo•Updated Sep 25, 2026Sep 25, 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+ 2

  bioinformaticsgenomicssurveillancecovid-19sars-cov-2

  HTML

  •

  GNU General Public License v3.0

  •2828 forks in BU-ISCIII/relecov-tools•88 stars in BU-ISCIII/relecov-tools•2727 issues in BU-ISCIII/relecov-tools•33 pull requests in BU-ISCIII/relecov-tools•Updated Sep 24, 2026Sep 24, 2026

• bd-tools

  Public
  Tools to process MePRAM data for ML

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •44 forks in BU-ISCIII/bd-tools•00 stars in BU-ISCIII/bd-tools•00 issues in BU-ISCIII/bd-tools•00 pull requests in BU-ISCIII/bd-tools•Updated Sep 23, 2026Sep 23, 2026

• relecov_2026_drylab_eqa

  Public
  Scripts to process the results from the 2026 RELECOV DryLab EQA

  Python

  •

  GNU General Public License v3.0

  •11 fork in BU-ISCIII/relecov_2026_drylab_eqa•00 stars in BU-ISCIII/relecov_2026_drylab_eqa•00 issues in BU-ISCIII/relecov_2026_drylab_eqa•11 pull request in BU-ISCIII/relecov_2026_drylab_eqa•Updated Sep 22, 2026Sep 22, 2026

• pathocore-api

  Public
  Core API for managing and serving data for pathogen platforms and related services.

  Python

  •

  GNU General Public License v3.0

  •33 forks in BU-ISCIII/pathocore-api•00 stars in BU-ISCIII/pathocore-api•00 issues in BU-ISCIII/pathocore-api•00 pull requests in BU-ISCIII/pathocore-api•Updated Aug 28, 2026Aug 28, 2026

• pathocore-web

  Public
  TypeScript

  •22 forks in BU-ISCIII/pathocore-web•00 stars in BU-ISCIII/pathocore-web•00 issues in BU-ISCIII/pathocore-web•00 pull requests in BU-ISCIII/pathocore-web•Updated Aug 4, 2026Aug 4, 2026

• beacon2-ri-tools-v2

  Public
  Python

  •

  Apache License 2.0

  •1919 forks in BU-ISCIII/beacon2-ri-tools-v2•00 stars in BU-ISCIII/beacon2-ri-tools-v2•00 issues in BU-ISCIII/beacon2-ri-tools-v2•00 pull requests in BU-ISCIII/beacon2-ri-tools-v2•Updated Jun 16, 2026Jun 16, 2026

• OmicsExplorer

  Public
  Sandra Sanchez Pinilla TFM

  R

  •11 fork in BU-ISCIII/OmicsExplorer•00 stars in BU-ISCIII/OmicsExplorer•00 issues in BU-ISCIII/OmicsExplorer•00 pull requests in BU-ISCIII/OmicsExplorer•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

  •55 forks in BU-ISCIII/virology_training•44 stars in BU-ISCIII/virology_training•00 issues in BU-ISCIII/virology_training•00 pull requests in BU-ISCIII/virology_training•Updated Mar 26, 2026Mar 26, 2026

• infectious-diseases-toolkit

  Public
  Infectious diseases toolkit

  Python

  •

  Other

  •4646 forks in BU-ISCIII/infectious-diseases-toolkit•11 star in BU-ISCIII/infectious-diseases-toolkit•00 issues in BU-ISCIII/infectious-diseases-toolkit•00 pull requests in BU-ISCIII/infectious-diseases-toolkit•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

  •22 forks in BU-ISCIII/flu_resistance•11 star in BU-ISCIII/flu_resistance•00 issues in BU-ISCIII/flu_resistance•00 pull requests in BU-ISCIII/flu_resistance•Updated Dec 15, 2025Dec 15, 2025

• nexstrain_relecov

  Public
  Python

  •

  MIT License

  •22 forks in BU-ISCIII/nexstrain_relecov•00 stars in BU-ISCIII/nexstrain_relecov•00 issues in BU-ISCIII/nexstrain_relecov•00 pull requests in BU-ISCIII/nexstrain_relecov•Updated Dec 10, 2025Dec 10, 2025

• galaxy_virologist_training

  Public
  Galaxy training for virology profiles

  HTML

  •44 forks in BU-ISCIII/galaxy_virologist_training•00 stars in BU-ISCIII/galaxy_virologist_training•22 issues in BU-ISCIII/galaxy_virologist_training•00 pull requests in BU-ISCIII/galaxy_virologist_training•Updated Nov 5, 2025Nov 5, 2025

• pdn_priority_pathogens

  Public
  Python

  •

  MIT License

  •55 forks in BU-ISCIII/pdn_priority_pathogens•22 stars in BU-ISCIII/pdn_priority_pathogens•00 issues in BU-ISCIII/pdn_priority_pathogens•00 pull requests in BU-ISCIII/pdn_priority_pathogens•Updated Oct 14, 2025Oct 14, 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

  •77 forks in BU-ISCIII/spanish-pathogens-portal•00 stars in BU-ISCIII/spanish-pathogens-portal•11 issue in BU-ISCIII/spanish-pathogens-portal•00 pull requests in BU-ISCIII/spanish-pathogens-portal•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

  •77 forks in BU-ISCIII/introduction_to_bioinformatics•44 stars in BU-ISCIII/introduction_to_bioinformatics•22 issues in BU-ISCIII/introduction_to_bioinformatics•00 pull requests in BU-ISCIII/introduction_to_bioinformatics•Updated Jun 12, 2025Jun 12, 2025

• pikavirus

  Public
  New pikavirus in dsl2

  Nextflow

  •

  MIT License

  •66 forks in BU-ISCIII/pikavirus•22 stars in BU-ISCIII/pikavirus•55 issues in BU-ISCIII/pikavirus•00 pull requests in BU-ISCIII/pikavirus•Updated Mar 26, 2025Mar 26, 2025

• PikaVirus_OLD

  Public
  Python

  •

  MIT License

  •33 forks in BU-ISCIII/PikaVirus_OLD•00 stars in BU-ISCIII/PikaVirus_OLD•00 issues in BU-ISCIII/PikaVirus_OLD•00 pull requests in BU-ISCIII/PikaVirus_OLD•Updated Mar 24, 2025Mar 24, 2025

• taranys

  Public
  cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

  sequencingmlstcgmlst+ 4

  sequencingmlstcgmlstoutbreak-detectionbacterial-genomeswgmlstoutbreak-data-analysis

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •66 forks in BU-ISCIII/taranys•99 stars in BU-ISCIII/taranys•33 issues in BU-ISCIII/taranys•00 pull requests in BU-ISCIII/taranys•Updated Jan 3, 2025Jan 3, 2025