Repositories list

• bd-tools

  Public

  BU-ISCIII/bd-tools’s past year of commit activity
  Tools to process MePRAM data for ML

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •44 forks•00 stars•00 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• mepram-api

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

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• impact-tools

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

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• iskylims

  Public

  BU-ISCIII/iskylims’s past year of commit activity
  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

  •4141 forks•9393 stars•1616 issues•33 pull requests•Updated May 19, 2026May 19, 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

  •2020 forks•44 stars•1515 issues•22 pull requests•Updated May 18, 2026May 18, 2026

• viralrecon

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

  Nextflow

  •

  MIT License

  •150150 forks•11 star•00 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• BU-ISCIII

  Public
  Our Wiki and main public documentation repository.

  documentationbioinformaticsbioinformatics-unit

  documentationbioinformaticsbioinformatics-unit

  1111 forks•77 stars•44 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• OmicsExplorer

  Public

  BU-ISCIII/OmicsExplorer’s past year of commit activity
  Sandra Sanchez Pinilla TFM

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• relecov-platform

  Public

  BU-ISCIII/relecov-platform’s past year of commit activity
  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•11 star•1818 issues•44 pull requests•Updated May 8, 2026May 8, 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•00 stars•00 issues•00 pull requests•Updated May 7, 2026May 7, 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

  •2929 forks•77 stars•2727 issues•55 pull requests•Updated Apr 30, 2026Apr 30, 2026

• virology_training

  Public
  This repo contains all the resources needed to follow the virology training to analyze viral sequencing data.

  HTML

  •55 forks•44 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• infectious-diseases-toolkit

  Public
  Infectious diseases toolkit

  Python

  •

  Other

  •4646 forks•11 star•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• beacon2-pi-api

  Public
  Beacon v2 Production Implementation (API)

  Python

  •

  Apache License 2.0

  •1414 forks•00 stars•00 issues•00 pull requests•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

  •22 forks•11 star•00 issues•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• nexstrain_relecov

  Public
  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Dec 10, 2025Dec 10, 2025

• LocalEGA

  Public
  A federated storage for sensitive data

  Python

  •

  Apache License 2.0

  •2222 forks•00 stars•00 issues•00 pull requests•Updated Nov 18, 2025Nov 18, 2025

• galaxy_virologist_training

  Public
  Galaxy training for virology profiles

  HTML

  •55 forks•00 stars•22 issues•00 pull requests•Updated Nov 5, 2025Nov 5, 2025

• pdn_priority_pathogens

  Public
  Python

  •

  MIT License

  •44 forks•11 star•00 issues•00 pull requests•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

  •44 forks•11 star•00 issues•00 pull requests•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

  •77 forks•00 stars•11 issue•00 pull requests•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•44 stars•22 issues•00 pull requests•Updated Jun 12, 2025Jun 12, 2025

• pikavirus

  Public
  New pikavirus in dsl2

  Nextflow

  •

  MIT License

  •77 forks•22 stars•55 issues•00 pull requests•Updated Mar 26, 2025Mar 26, 2025

• PikaVirus_OLD

  Public
  Python

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•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•99 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 27, 2024Nov 27, 2024

• bacass

  Public
  Simple bacterial assembly and annotation pipeline

  Nextflow

  •

  MIT License

  •7272 forks•00 stars•00 issues•00 pull requests•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+ 7

  genomenextflowsequencingwgsngs-analysisoutbreak-detectionbacterial-genomesoutbreaksbacterial-wgs-trainingwgs-analysis

  HTML

  •

  GNU General Public License v3.0

  •22 forks•44 stars•11 issue•00 pull requests•Updated Oct 31, 2024Oct 31, 2024

• buisciii.github.io

  Public
  BU-ISCIII team website

  SCSS

  •

  MIT License

  •2.7k2.7k forks•00 stars•00 issues•00 pull requests•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

  •22 forks•33 stars•00 issues•00 pull requests•Updated Feb 28, 2024Feb 28, 2024