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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

dissertation

XeLaTeX source for my PhD thesis

distats

Calculate distance statistics for an alignment

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

dotfiles

Files and directories starting with a dot (config files)

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

hamstrad

Heavily modified version of HaMStR (Ebersberger et al., 2009)

horizontal-te-transfer

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

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.

meuselblast

skim through BLAST result files and process information therein

mobilome

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

myscripts

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

orthograph

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

orthograph-test-data

Test data for Orthograph

qmk_firmware

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

samplot

Plot structural variant signals from many BAMs and CRAMs

sat-assembler

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

scripts

Various scripts for various purposes

snakemake-hpc-teaching-material

snakemake-wrappers

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

survivor

Toolset for SV simulation, comparison and filtering

thesis

LaTeX source of my diploma thesis