Kristian Ullrich's repositories
bio-scripts
collection of scripts for bioinformatic analysis
oggmap
oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
literal-dists
Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix
openBIS-UGM2025
Topics proposed for hackaton sessions at openBIS UGM 2025
awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
bacterial-short-snake
Snakemake-powered commandline tool to do bacterial genome assembly, annotation and reference-based comparison using short-reads.
bioconda-recipes
Conda recipes for the bioconda channel.
Broccoli
orthology assignment using phylogenetic and network analyses
carpentries-workshop-template
The Carpentries Workshop Template
circlize
Circular visualization in R
DEEPSPACE
Whole genome visualization and comparative genomics in R
dist2bionjs
Use stdin distance matrix to calculate bionjs
gabi
Genomic Analysis of Bacterial Isolates
msmc-tools
Tools and Utilities for msmc and msmc2
nf-template
A template for a creating a new nextflow pipeline project.
PolyPanner
Leveraging dense temporal sampling to improve assembly quality and identify high confidence polymorphic variants.
pwalign
Perform pairwise sequence alignments
syntenyPlotteR
R package to draw syntenic plots in 3 different styles
TOFU-MAaPO
Nextflow pipeline for the analysis of metagenomic short reads.
vcfppR
The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049
xenoseq
Pipeline to automate the comparison between short-read libraries to detect foreign ("xenotypic") sequences.