Methods for Computational Genomics (GitHub profile)

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

install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1016/j.xgen.2023.100281

Wally: Visualization of aligned sequencing reads and contigs.

install with bioconda Anaconda-Server Badge GitHub license GitHub Releases DOI:10.1016/j.xgen.2023.100281

Lorax: A long-read analysis toolbox for cancer genomics

GitHub license GitHub Releases DOI:10.1016/j.xgen.2023.100281

Rayas: Discovery of templated insertion threads

Web applications for Molecular Biologists

www.gear-genomics.com

GitHub stars GitHub forks DOI:10.1186/s12864-020-6635-8

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

GitHub stars GitHub forks DOI:10.1093/bioinformatics/bty1007

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

Analysis Pipelines for Computational Genomics

GitHub stars GitHub forks DOI:10.15252/emmm.202012104

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

GitHub stars GitHub forks DOI:10.3324/haematol.2015.129692

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

GitHub stars GitHub forks DOI:10.1016/j.meegid.2024.105577

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 contribute to is available on GitHub.