Methods for Computational Genomics (GitHub profile)
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
Wally: Visualization of aligned sequencing reads and contigs.
Lorax: A long-read analysis toolbox for cancer genomics
Rayas: Discovery of templated insertion threads
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.
SARS-CoV-2 Analysis Pipeline: Computational workflow to analyze short-read, whole-genome SARS-CoV-2 data.
GitHub Code Repositories
A full list of open-source software projects I contributed to is available on GitHub.