pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data

general workflow for genome assembly-based SNP phylogeny with optional recombination masking

IPARUS (Integrated Platform for Parus Alignments, Resources and Useful Sequences) is a web-based genomic resource & analysis platform developed at the Gossmann Lab.

Reusable bacterial genome mining pipeline for assembled genome FASTA files using QUAST, Bakta, antiSMASH, GECCO, and combined BGC summary reporting.

Tutorial for Polygenic Risk Score development

An agentic AI pipeline for annotating genetic variants, linking them to disease evidence, and generating structured interpretation reports using biomedical APIs and LLM reasoning.

An end-to-end Pan-Genome Wide Association Study (Pan-GWAS) and algorithmic phenotyping pipeline. Designed to map horizontal gene transfer networks and pinpoint absolute drivers of antimicrobial resistance (AMR), featuring interactive 3D structural and topological modeling of Campylobacter jejuni.

Reusable bacterial genome analysis pipeline for paired-end FASTQ data using FastQC, fastp, SPAdes, QUAST, Prokka, and MultiQC.

ExomeFlow is a Python package that provides a complete, automated Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally annotated variants in a single reproducible CLI command.

Reusable comparative bacterial genomics pipeline for assembled bacterial genome FASTA files using QUAST, Bakta, FastANI, Panaroo, and FastTree.

SeqForge: a modular, bash-based bioinformatics pipeline designed for the complete processing of paired-end (PE) sequencing data from Illumina technologies, culminating in highly filtered genetic variant calls.