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aminoextract

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

ampligone

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

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

auriclass

Quick estimation of Candida auris clade using mash

bioconda-recipes

Conda recipes for the bioconda channel.

clcbioformatter

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

containers

Creating and uploading containers to ghcr

hera-bioinformatics-training

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

irods_rename

Rename files from an iRODS collection

juno-amr

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juno-annotation

Annotation of chromosomes and plasmids of bacteria (AMR group)

juno-assembly

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

juno-assembly-verification

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-clustering

Pipeline to cluster cgMLST or SNP data

juno-library

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

juno-mapping

Reference-based mapping Juno pipeline

juno-population

juno-seroba

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

juno-snp

Pipeline to perform SNP analysis in bacterial samples.

juno-typing

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

juno-variant-typing

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

juno_pipeline_ion

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

myco_lofreq

Pipeline to call minority variants in Mycobacterium samples

refsampr

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