Repositories list

• juno-amr

  Public
  -

  Python

  •

  GNU Affero General Public License v3.0

  •1•1•0•0•Updated Dec 18, 2024Dec 18, 2024

• ViroConstrictor

  Public
  ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

  pythonbioinformaticssnakemake+ 8public-healthvirusesvirologyngs-analysissnakemake-workflowrivmconsensus-sequences+ 1

  Python

  •

  GNU Affero General Public License v3.0

  •2•5•3•2•Updated Dec 18, 2024Dec 18, 2024

• juno-library

  Public
  Package containing the basic classes that are used as base for the wrappers of the other Juno pipelines

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• juno-typing

  Public
  Pipeline to perform bacterial typing (7-locus MLST and serotyping when appropriate). It works with several (but not all) species/genera.

  Python

  •

  GNU Affero General Public License v3.0

  •0•4•1•1•Updated Dec 3, 2024Dec 3, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• juno-mapping

  Public
  Reference-based mapping Juno pipeline

  Python

  •0•1•0•0•Updated Nov 18, 2024Nov 18, 2024

• AmpliGone

  Public
  A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

  pythonbioinformaticsnanopore+ 5pcrilluminangs-analysisamplicon-sequencingrivm

  Python

  •

  GNU Affero General Public License v3.0

  •0•13•3•2•Updated Nov 12, 2024Nov 12, 2024

• AminoExtract

  Public
  AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input

  pythonbioinformaticsngs-analysis

  Python

  •

  MIT License

  •0•1•1•0•Updated Sep 25, 2024Sep 25, 2024

• in-silico-mlva

  Public
  Tool to determine in-silico MLVA for MRSA isolates

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• Submission-Assembler

  Public
  Snakemake workflow to assemble long read data

  C

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• juno-variant-typing

  Public
  Juno pipeline for the interpretation of variants identified through reference-based mapping

  Python

  •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

• juno-assembly

  Public
  Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics

  Python

  •

  GNU Affero General Public License v3.0

  •5•3•0•0•Updated Aug 1, 2024Aug 1, 2024

• juno-clustering

  Public
  Pipeline to cluster cgMLST or SNP data

  Python

  •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• skiml-cluster

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• SARS2seq

  Public
  SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

  pythonsnakemakepublic-health+ 9virusesvirologyngs-analysissnakemake-workflowrivmconsensus-sequencescoronavirus+ 2

  Python

  •

  GNU Affero General Public License v3.0

  •0•6•2•1•Updated Jul 3, 2024Jul 3, 2024

• juno-snp

  Public
  Pipeline to perform SNP analysis in bacterial samples.

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•1•Updated Jun 27, 2024Jun 27, 2024

• juno-population

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated Jun 14, 2024Jun 14, 2024

• apollo-variant-typing

  Public
  Apollo pipeline for the interpretation of variants identified through reference-based mapping

  Python

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

• apollo-mapping

  Public
  Reference mapping workflow for the analysis of fungal samples

  Python

  •

  GNU Affero General Public License v3.0

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

• irods_rename

  Public
  Rename files from an iRODS collection

  Python

  •0•0•0•0•Updated May 31, 2024May 31, 2024

• juno-cgmlst

  Public
  Pipeline to perform cgMLST (or wgMLST) analysis. At the moment it just handles few genera for cgMLST

  Python

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated May 21, 2024May 21, 2024

• HERA-Bioinformatics-Training

  Public
  Jupyter Notebook

  •1•2•0•0•Updated May 10, 2024May 10, 2024

• HERA-workshop-StMaarten

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Mar 12, 2024Mar 12, 2024

• TrueConsense

  Public
  TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time

  bioinformaticsvirologyngs-analysis+ 1consensus-calling

  Python

  •

  GNU Affero General Public License v3.0

  •1•5•1•0•Updated Feb 7, 2024Feb 7, 2024

• auriclass

  Public
  Quick estimation of Candida auris clade using mash

  Python

  •

  GNU Affero General Public License v3.0

  •1•6•0•0•Updated Oct 27, 2023Oct 27, 2023

• juno-assembly-verification

  Public
  Python

  •0•0•0•0•Updated Jul 26, 2023Jul 26, 2023

• juno-annotation

  Public
  Annotation of chromosomes and plasmids of bacteria (AMR group)

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•1•Updated Jul 20, 2023Jul 20, 2023

• Juno-seroba

  Public
  Pipeline for serotyping Streptococcus pneumoniae (to be merged in Juno-typing).

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jul 20, 2023Jul 20, 2023

• juno-blast

  Public
  Automated BLASTing from fasta files.

  Python

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated Jul 18, 2023Jul 18, 2023

• clcbioformatter

  Public
  Re-formatting Fasta headers to fit CLC bio. Requested by the AMR group.

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Jun 30, 2023Jun 30, 2023