Projects

Our group develops software and tools in different areas. Below we provide links to different resources. Most of our code is freely accessible and open source. If not specificially stated, we apply a MIT License, i.e. our software is provided as is and without warranties of any kind:

CADD - Combined Annotation Dependent Depletion (CADD) framework to score the deleteriousness of single nucleotide variants, multi-allelic substitutions and short insertion/deletions in the human genome (GRCh37/38).

CADD scripts - Offline tool to score the deleteriousness of single nucleotide variants, multi-allelic substitutions and short insertion/deletions in the human genome in an on-site installation.

CADD US webserver - US-based server for easy scoring, data access and download of pre-calculated CADD scores.

ReMM Score - The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variants (SNVs and small InDels) in the human genome (GRCh37/GRCh38) in terms of Mendelian diseases.

CADD-SV - CADD-SV is a framework to estimate the impact of Structural Variants (SVs) in the human genome. We combine various annotations to predict the deleteriousness of human deletions. We provide a webserver for easy scoring and download of pre-scored SVs.

CADD-SV scripts - Offline tool to score the deleteriousness of structural variants (SVs, i.e. large insertions, deletions and duplications) in the human genome.

MPRAsnakeflow - Snakemake-based pipeline to processes sequencing data from Massively Parallel Reporter Assays (MPRAs).

hemoMIPs - Molecular Inversion Probe (MIP) based targeted sequencing analysis and result reporting pipeline for hemophilia.

Saturation mutagenesis MPRA - Visualization of MPRA data for 20 disease-associated regulatory elements (enhancers and promoters) and one ultra conserved element.

MPRAflow (+documentation) - Nextflow-based pipeline to processes sequencing data from Massively Parallel Reporter Assays (MPRAs).

Cell-free DNA workflows - Workflows for analyzing epigenetic signals captured by fragmentation patterns of cell-free DNA.

Cell-free DNA analysis - analysis scripts for the epigenetic signals studied in our Cell 2016 (M. Snyder, M. Kircher et al.) cell-free DNA publication.

IBIS - accurate, fast and easy-to-use base caller for the Illumina sequencing system

freeIBIS - reimplementation of IBIS using an open source SVM library for accurate, fast and easy-to-use base calling on the Illumina sequencing system

index design - index design and analysis software for highly multiplexed target capture and sequencing.