Pinned Repositories
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
Infectieziekteonderzoek, Diagnostiek en laboratorium Surveillance-Bioinformatics (RIVM, The Netherlands)'s Repositories
RIVM-bioinformatics/Myco_lofreq
Pipeline to call minority variants in Mycobacterium samples
RIVM-bioinformatics/ids_bacteriology_man
Code for the website used for documenting bacteriology pipelines (tailor made for RIVM people). Written in R (bookdown)
RIVM-bioinformatics/Juno_pipeline_ion
Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics(iontorrent edition)
RIVM-bioinformatics/refsampr
Internal R package (for RIVM) for making quality control reports of reference samples. Different assembly metrics are followed up and plotted over time.
RIVM-bioinformatics/VirASM
VirASM is a quick and minimal pipeline to assemble metagenomics/viromics samples from illumina data
RIVM-bioinformatics/wgs_identification
Ramon WGS project pipeline