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    68 repositories

    • 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, processing, validation and upload to public databases, as well as analysis runs and database storage.
      bioinformaticsgenomicssurveillancecovid-19sars-cov-2
      Python
      •
      GNU General Public License v3.0
      •23•5•26•2•Updated Dec 23, 2024Dec 23, 2024

    • buisciii-tools

      Public
      set of helper tools for bu-isciii management of its core services portfolio.
      portfolioservicesbioinformaticsgenomicscore-servicesbioinformatics-analysis
      Python
      •
      GNU General Public License v3.0
      •13•1•21•1•Updated Dec 23, 2024Dec 23, 2024

    • relecov-platform

      Public
      Python
      •
      GNU General Public License v3.0
      •6•1•13•2•Updated Dec 20, 2024Dec 20, 2024

    • BU-ISCIII

      Public
      Our Wiki and main public documentation repository.
      documentationbioinformaticsbioinformatics-unit
      9•3•8•0•Updated Dec 20, 2024Dec 20, 2024

    • virology_training

      Public
      This repo contains all the resources needed to follow the virology training to analyze viral sequencing data.
      HTML
      •3•4•0•0•Updated Dec 16, 2024Dec 16, 2024

    • viralrecon

      Public
      Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      •
      MIT License
      •113•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • infectious-diseases-toolkit

      Public
      Infectious diseases toolkit
      Python
      •
      Other
      •40•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • iskylims

      Public
      is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
      ngsngs-analysisngs-dataworkflowlimsbioinformatics-analysis
      Python
      •
      GNU General Public License v3.0
      •35•72•35•3•Updated Nov 15, 2024Nov 15, 2024

    • galaxy_virologist_training

      Public
      Galaxy training for virology profiles
      HTML
      •3•0•2•0•Updated Nov 15, 2024Nov 15, 2024

    • bacass

      Public
      Simple bacterial assembly and annotation pipeline
      Nextflow
      •
      MIT License
      •42•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.
      genomesequencingwgsngs-analysisoutbreak-detectionbacterial-genomesoutbreaksnextflowbacterial-wgs-trainingwgs-analysis
      HTML
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Oct 31, 2024Oct 31, 2024

    • 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
      •3•3•0•0•Updated Jun 21, 2024Jun 21, 2024

    • buisciii.github.io

      Public
      BU-ISCIII team website
      SCSS
      •
      MIT License
      •2.6k•0•0•0•Updated May 20, 2024May 20, 2024

    • taranis

      Public
      cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
      sequencingmlstcgmlstoutbreak-detectionbacterial-genomeswgmlstoutbreak-data-analysis
      Python
      •
      GNU General Public License v3.0
      •4•7•0•0•Updated May 2, 2024May 2, 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
      •1•1•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+(MIGRATION)
      Python
      •
      MIT License
      •0•0•0•0•Updated May 26, 2023May 26, 2023

    • nexstrain_relecov

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2023Feb 13, 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
      1•0•0•0•Updated Nov 8, 2022Nov 8, 2022

    • assemblybacterias

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 26, 2022Sep 26, 2022

    • relecov_biohackaton

      Public
      11•0•9•0•Updated Jul 21, 2022Jul 21, 2022

    • 16S-Qiime-protocol

      Public
      Pipeline del análisis comenzado el día 4 de mayo de 2021, tema: "bloqueadores"
      Python
      •1•0•0•0•Updated Jul 6, 2022Jul 6, 2022

    • relecov_qc_exercise

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 20, 2022Jun 20, 2022

    • bacterial_assembly-nf

      Public
      Haploid bacterial assembly and automatic annotation implemented using Nextflow
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • bu-hack-a-isciii

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 16, 2022Feb 16, 2022

    • markdowns

      Public
      repository with the markdowns of all of our analyses.
      Python
      •1•1•0•0•Updated Jan 18, 2022Jan 18, 2022

    • PikaVirus

      Public
      Python
      •
      MIT License
      •1•0•3•0•Updated Jan 14, 2022Jan 14, 2022

    • download_bigsdb_api

      Public
      Script for interactive download schemas and definitions for any bigsdb installation using its api. Useful for downloading wg/cgMLST genes and alleles.
      rest-apipython3bigsdballelescgmlst-genesbigsdb-installation
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 21, 2021Dec 21, 2021

    • genebygenebact

      Public
      Gene-by-gene outbreaks analysis pipeline using cgMLST schemas
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • all_YML_files

      Public
      Compilation of all the YAML files used in the unit (both for backup and sharing purposes)
      0•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • iSkyLIMS_wetlab

      Public archive
      This repository contains a internal web page for sequencing runs management for NextSeq and MiSeq Illumina machines.
      limsngsdjango-projectngs-dataiskylims
      Python
      •2•5•10•0•Updated Aug 26, 2021Aug 26, 2021