Methods for Computational Genomics


install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1093/bioinformatics/bts378

Delly: Structural variant discovery by integrated paired-end and split-read analysis.


install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1093/bioinformatics/bty1007

Alfred: BAM alignment statistics, feature counting and feature annotation


install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1186/s12864-020-6635-8

Tracy: Basecalling, alignment and deconvolution of Sanger Chromatogram trace files.


install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1186/s12864-020-6635-8

Dicey: In-silico PCR and variant primer design


GitHub license GitHub Releases

rdxon: Rapid method to filter FASTQ files for reads containing k-mers absent in the entire 1000 Genomes sequencing data. Suitable to discover disease-causing mutations in rare disorders independent of any reference genome.


GEAR: www.gear-genomics.com

GitHub stars GitHub forks

Indigo: Variant Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products


GitHub stars GitHub forks

Alfred: Interactive, multi-sample and read-group aware quality control browser for NGS data.


Analysis Pipelines for Computational Genomics

GitHub stars GitHub forks

ATAC-Seq Pipeline: Computational Workflow to analyze ATAC-Seq data.


GitHub stars GitHub forks

DNA Variant Calling: Computational Workflow to analyze DNA whole-genome data and targeted NGS data.


GitHub Code Repositories

A full list of software projects I contributed to is available on GitHub.