BU-ISCIII

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67 repositories

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.
ngs ngs-analysis ngs-data workflow lims bioinformatics-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
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.
bioinformatics genomics surveillance covid-19 sars-cov-2
Python
•
GNU General Public License v3.0
•21•5•17•1•Updated Nov 14, 2024Nov 14, 2024
relecov-platform
Public
Python
•
GNU General Public License v3.0
•5•1•11•1•Updated Nov 14, 2024Nov 14, 2024
buisciii-tools
Public
set of helper tools for bu-isciii management of its core services portfolio.
portfolio services bioinformatics genomics core-services bioinformatics-analysis
Python
•
GNU General Public License v3.0
•12•1•15•0•Updated Nov 14, 2024Nov 14, 2024
BU-ISCIII
Public
Our Wiki and main public documentation repository.
documentation bioinformatics bioinformatics-unit
8•3•2•0•Updated Nov 14, 2024Nov 14, 2024
bacass
Public
Simple bacterial assembly and annotation pipeline
Nextflow
•
MIT License
•42•0•0•0•Updated Nov 6, 2024Nov 6, 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 Nov 5, 2024Nov 5, 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.
genome sequencing wgs ngs-analysis outbreak-detection bacterial-genomes outbreaks nextflow bacterial-wgs-training wgs-analysis
HTML
•
GNU General Public License v3.0
•0•2•1•0•Updated Oct 31, 2024Oct 31, 2024
viralrecon
Public
Assembly and intrahost/low-frequency variant calling for viral samples
Nextflow
•
MIT License
•112•0•0•0•Updated Oct 25, 2024Oct 25, 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.
sequencing mlst cgmlst outbreak-detection bacterial-genomes wgmlst outbreak-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
•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-api python3 bigsdb alleles cgmlst-genes bigsdb-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
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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.
lims ngs django-project ngs-data iskylims
Python
•2•5•10•0•Updated Aug 26, 2021Aug 26, 2021
iSkyLIMS_drylab
Public archive
lims ngs django-project ngs-data iskylims
Python
•5•2•3•0•Updated Aug 26, 2021Aug 26, 2021