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

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.

auriclass

Quick estimation of Candida auris clade using mash

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

juno-typing

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

juno-assembly

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

HERA-Bioinformatics-Training

AminoExtract

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

containers

Creating and uploading containers to ghcr

juno-amr

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juno-blast

Automated BLASTing from fasta files.

juno-cgmlst

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

juno-mapping

Reference-based mapping Juno pipeline

juno-population

juno-library

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

apollo-mapping

Reference mapping workflow for the analysis of fungal samples

apollo-variant-typing

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

bioconda-recipes

Conda recipes for the bioconda channel.

clcbioformatter

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

HERA-workshop-StMaarten

ids_bacteriology_man

Code for the website used for documenting bacteriology pipelines (tailor made for RIVM people). Written in R (bookdown)

in-silico-mlva

juno-annotation

Annotation of chromosomes and plasmids of bacteria (AMR group)

juno-assembly-verification

Juno-seroba

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

juno-snp

Pipeline to perform SNP analysis in bacterial samples.

Juno_pipeline_ion

Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics(iontorrent edition)

refsampr

Internal R package (for RIVM) for making quality control reports of reference samples. Different assembly metrics are followed up and plotted over time.

skiml-cluster