hoelzer

dfg

A LaTeX template for a basic DFG (Deutsche Forschungsgemeinschaft, German Research Foundation) grant proposal.

pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.

mgnify-lr

Evaluation of long-read support for the MGnify pipeline

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.

sankey

Build a Sankey plot from an input CSV file

2021-04-12_treemap

faltwerk

A library for spatial exploratory data analysis of protein structures

nf-minimap2

A small Nextflow example using minimap2.

sc2-consensus-mutation-profile

bed2bedpe

A simple py script from github.com/rki-mf1/covpipe2

covid_snp_catalogue

A small, rather hacky, script that takes a bunch of SARS-CoV-2 genomes and compares them to the RefSeq genome.

CV.js

D3/Bootstrap CV generator

CWL_viral_pipeline

dammit-nf

Containerized Nextflow implementation of the dammit de novo transcriptome annotation pipeline (http://dib-lab.github.io/dammit/)

darkq

A message queue for genomic surveillance

docker-compose-tutorial

EpiDope

Prediction of B-cell epitopes from amino acid sequences using deep neural networks.

EpiDope-1

Prediction of B-cell epitopes from amino acid sequences using deep neural networks.

fieldbioinformatics

The ARTIC field bioinformatics pipeline

init

Initialize a new bioinformatics project structure and git control

mag

Assembly and binning of metagenomes

misc

A collection of littler helpers

nf-hmmsearch

A simple Nextflow workflow to perform hmmsearch on a given input set of genomes and HMMs

nf_example

A small example workflow to introduce Nextflow and Docker integration

phd-thesis

My PhD thesis from the University of Jena

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

sc2-selection

Positive selection analyses for SARS-CoV-2

varVAMP

Design primers for highly diverse viruses!

wuhan