mptrsen

Orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models

scripts

Various scripts for various purposes

distats

Calculate distance statistics for an alignment

dissertation

XeLaTeX source for my PhD thesis

horizontal-TE-transfer

Horizontal transfer of unclassified TEs in insects -- helper scripts and other tools

mobilome

TE annotation pipeline and analysis scripts for the insect mobilome publication by Petersen et al.

samplot

Plot structural variant signals from many BAMs and CRAMs

dotfiles

Files and directories starting with a dot (config files)

snakemake-hpc-teaching-material

trichodes

Snakemake pipeline to infer a phylogeny from genome skimming data

1kite-script-collection

Scripts for all steps in the 1KITE analysis pipeline

bash-sensible

An attempt at saner Bash defaults

bioconda-recipes

Conda recipes for the bioconda channel.

canu

A single molecule sequence assembler for genomes large and small.

circlator

A tool to circularize genome assemblies

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

gatk-variant-calling

Clone of the Snakemake workflow for variant calling with the GATK pipeline

gfalign

Assembly graph read alignment and analysis

isONclust

Conda recipe for isONclust, a tool for clustering PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters

kollector

de novo targeted gene assembly

LatexBeamerThemeUniBonnStyle

Latex beamer template in Uni Bonn style.

myScripts

A bunch of non-generic scripts that I use in my projects

Orthograph-test-data

Test data for Orthograph

qmk_firmware

Open-source keyboard firmware for Atmel AVR and Arm USB families

SAT-Assembler

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data)

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

SURVIVOR

Toolset for SV simulation, comparison and filtering

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

wesanderson

A Wes Anderson color palette for R