Infectieziekteonderzoek, Diagnostiek en laboratorium Surveillance-Bioinformatics (RIVM, The Netherlands)

AmpliGone

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

auriclass

Quick estimation of Candida auris clade using mash

containers

Creating and uploading containers to ghcr

HERA-Bioinformatics-Training

juno-assembly

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

juno-typing

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

Myco_lofreq

Pipeline to call minority variants in Mycobacterium samples

SARS2seq

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.

TrueConsense

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

ViroConstrictor

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

RIVM-bioinformatics/AmpliGone

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

RIVM-bioinformatics/SARS2seq

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.

RIVM-bioinformatics/auriclass

Quick estimation of Candida auris clade using mash

RIVM-bioinformatics/TrueConsense

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

RIVM-bioinformatics/ViroConstrictor

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

RIVM-bioinformatics/juno-typing

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

RIVM-bioinformatics/juno-assembly

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

RIVM-bioinformatics/HERA-Bioinformatics-Training

RIVM-bioinformatics/AminoExtract

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

RIVM-bioinformatics/containers

Creating and uploading containers to ghcr

RIVM-bioinformatics/juno-amr

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RIVM-bioinformatics/juno-blast

Automated BLASTing from fasta files.

RIVM-bioinformatics/juno-cgmlst

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

RIVM-bioinformatics/juno-mapping

Reference-based mapping Juno pipeline

RIVM-bioinformatics/juno-population

RIVM-bioinformatics/in-silico-mlva

RIVM-bioinformatics/juno-annotation

Annotation of chromosomes and plasmids of bacteria (AMR group)

RIVM-bioinformatics/juno-library

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

RIVM-bioinformatics/apollo-mapping

Reference mapping workflow for the analysis of fungal samples

RIVM-bioinformatics/apollo-variant-typing

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

RIVM-bioinformatics/bioconda-recipes

Conda recipes for the bioconda channel.

RIVM-bioinformatics/clcbioformatter

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

RIVM-bioinformatics/HERA-workshop-StMaarten

RIVM-bioinformatics/irods_rename

Rename files from an iRODS collection

RIVM-bioinformatics/juno-assembly-verification

RIVM-bioinformatics/juno-clustering

Pipeline to cluster cgMLST or SNP data

RIVM-bioinformatics/Juno-seroba

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

RIVM-bioinformatics/juno-snp

Pipeline to perform SNP analysis in bacterial samples.

RIVM-bioinformatics/juno-variant-typing

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

RIVM-bioinformatics/skiml-cluster