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/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