Pinned Repositories
emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
ribap
A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
rnaflow
A simple RNA-Seq differential gene expression pipeline using Nextflow
dfg
A LaTeX template for a basic DFG (Deutsche Forschungsgemeinschaft, German Research Foundation) grant proposal.
mgnify-lr
Evaluation of long-read support for the MGnify pipeline
nanovirus
A nextflow implementation of the assembly-free detection of viruses from nanopore data
pocp
Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
virify
A Nextflow implementation of the EBI VIRify pipeline for the detection of viruses from metagenomic assemblies.
visual
A collection of small scripts for data visualisation.
clean
A nextflow pipeline for decontamination of short reads, long reads and contigs
hoelzer's Repositories
hoelzer/dfg
A LaTeX template for a basic DFG (Deutsche Forschungsgemeinschaft, German Research Foundation) grant proposal.
hoelzer/pocp
Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
hoelzer/mgnify-lr
Evaluation of long-read support for the MGnify pipeline
hoelzer/virify
A Nextflow implementation of the EBI VIRify pipeline for the detection of viruses from metagenomic assemblies.
hoelzer/visual
A collection of small scripts for data visualisation.
hoelzer/sankey
Build a Sankey plot from an input CSV file
hoelzer/2021-04-12_treemap
hoelzer/faltwerk
A library for spatial exploratory data analysis of protein structures
hoelzer/nf-minimap2
A small Nextflow example using minimap2.
hoelzer/sc2-consensus-mutation-profile
hoelzer/2024-Lecture-Nanopore-Assembly
A practical introduction to long-read bioinformatics for bacterial genome reconstruction.
hoelzer/bed2bedpe
A simple py script from github.com/rki-mf1/covpipe2
hoelzer/covid_snp_catalogue
A small, rather hacky, script that takes a bunch of SARS-CoV-2 genomes and compares them to the RefSeq genome.
hoelzer/CV.js
D3/Bootstrap CV generator
hoelzer/dammit-nf
Containerized Nextflow implementation of the dammit de novo transcriptome annotation pipeline (http://dib-lab.github.io/dammit/)
hoelzer/darkq
A message queue for genomic surveillance
hoelzer/docker-compose-tutorial
hoelzer/docker_pipelines
Nextflow/Docker pipelines for "easy use"
hoelzer/EpiDope-1
Prediction of B-cell epitopes from amino acid sequences using deep neural networks.
hoelzer/fieldbioinformatics
The ARTIC field bioinformatics pipeline
hoelzer/hoelzer
My profile.
hoelzer/hoelzer.github.io
My academic personal web page.
hoelzer/init
Initialize a new bioinformatics project structure and git control
hoelzer/mag
Assembly and binning of metagenomes
hoelzer/nf-hmmsearch
A simple Nextflow workflow to perform hmmsearch on a given input set of genomes and HMMs
hoelzer/nf_example
A small example workflow to introduce Nextflow and Docker integration
hoelzer/phd-thesis
My PhD thesis from the University of Jena
hoelzer/SARS-CoV-2-Sequenzdaten_aus_Deutschland
Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermitteln
hoelzer/sc2-selection
Positive selection analyses for SARS-CoV-2
hoelzer/varVAMP
Design primers for highly diverse viruses!