Methods for Computational Genomics
Delly: Structural variant discovery by integrated paired-end and split-read analysis.
Alfred: BAM alignment statistics, feature counting and feature annotation
Tracy: Basecalling, alignment and deconvolution of Sanger Chromatogram trace files.
Dicey: In-silico PCR and variant primer design
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.
Indigo: Variant Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
Alfred: Interactive, multi-sample and read-group aware quality control browser for NGS data.
Analysis Pipelines for Computational Genomics
ATAC-Seq Pipeline: Computational Workflow to analyze ATAC-Seq data.
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.