Repositories list

• 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.

  bioinformaticsgenomicssurveillance+ 2covid-19sars-cov-2

  Python

  •

  GNU General Public License v3.0

  •21•5•21•2•Updated Oct 11, 2024Oct 11, 2024

• relecov-platform

  Public
  Python

  •

  GNU General Public License v3.0

  •5•1•7•0•Updated Oct 9, 2024Oct 9, 2024

• BU-ISCIII

  Public
  Our Wiki and main public documentation repository.

  documentationbioinformaticsbioinformatics-unit

  7•2•2•0•Updated Oct 3, 2024Oct 3, 2024

• buisciii-tools

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

  portfolioservicesbioinformatics+ 3genomicscore-servicesbioinformatics-analysis

  Python

  •

  GNU General Public License v3.0

  •12•1•17•0•Updated Oct 1, 2024Oct 1, 2024

• viralrecon

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

  Nextflow

  •

  MIT License

  •108•0•0•0•Updated Sep 17, 2024Sep 17, 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-data+ 3workflowlimsbioinformatics-analysis

  Python

  •

  GNU General Public License v3.0

  •35•71•34•4•Updated Sep 3, 2024Sep 3, 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

  •2.5k•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.

  sequencingmlstcgmlst+ 4outbreak-detectionbacterial-genomeswgmlstoutbreak-data-analysis

  Python

  •

  GNU General Public License v3.0

  •3•7•0•0•Updated May 2, 2024May 2, 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 Apr 4, 2024Apr 4, 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

• galaxy_virologist_training

  Public
  Galaxy training for virology profiles

  HTML

  •2•0•2•0•Updated Nov 15, 2023Nov 15, 2023

• 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

  •2•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-apipython3bigsdb+ 3allelescgmlst-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-project+ 2ngs-dataiskylims

  Python

  •2•5•10•0•Updated Aug 26, 2021Aug 26, 2021

• iSkyLIMS_drylab

  Public archive
  limsngsdjango-project+ 2ngs-dataiskylims

  Python

  •5•2•3•0•Updated Aug 26, 2021Aug 26, 2021

• iSkyLIMS_core

  Public archive
  iSkyLIMS home website for information and links purposes

  limsngsdjango-project+ 2ngs-dataiskylims

  CSS

  •1•1•1•0•Updated Aug 26, 2021Aug 26, 2021

• iSkyLIMS_clinic

  Public archive
  CSS

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Aug 26, 2021Aug 26, 2021