florianzwagemaker
I build software for analyzing viruses at the Dutch National Institute for Public Health and the Environment (RIVM) @RIVM-bioinformatics
Center for Infectious Disease ControlUtrecht, The Netherlands
Pinned Repositories
Jovian_archive
Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
augur
Pipeline components for real-time phylodynamic analysis
bioconda-recipes
Conda recipes for the bioconda channel.
colab_test
jovian-docs
Documentation site for the Jovian genomics toolkit
SoftClipper
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.
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
florianzwagemaker's Repositories
florianzwagemaker/SoftClipper
florianzwagemaker/jovian-docs
Documentation site for the Jovian genomics toolkit
florianzwagemaker/augur
Pipeline components for real-time phylodynamic analysis
florianzwagemaker/bioconda-recipes
Conda recipes for the bioconda channel.
florianzwagemaker/colab_test
florianzwagemaker/gffpandas
Parse GFF3 into Pandas dataframes
florianzwagemaker/Juno-amr
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florianzwagemaker/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
florianzwagemaker/Porechop
adapter trimmer for Oxford Nanopore reads
florianzwagemaker/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
florianzwagemaker/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
florianzwagemaker/ViroConstrictor-tst
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