CV of Simon Heumos

Coffy's web service with a RESTful API. No coffee without a coffee machine.

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

Genotyping lots of samples with big pangenomes

Statistics and analysis for variation graphs

strange cross-platform, performance-oriented and interactive pangenome and large graph visualization

a nextflow pipeline for creating a pangenome with minigraph-cactus

High Performance Sorting Based Distributed memory K-mer counter

Computational Pangenomics in Memphis

upload big files to Zenodo using cURL, jq and bash

Experimental features for Nextflow

A Nextflow plugin to estimate the CO₂ footprint of pipeline runs.

Yet another LLM command line interface

lace up GFA files using panSN path name sub-ranges to coordinate the lacing

A toolkit for exploring regions of variation in a variation graph

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Personal Cancer Genome Reporter (PCGR)

Pipeline to fetch metadata and raw FastQ files from public databases

Single-cell perturbation analysis

Identification of transposable element families from pangenome polymorphisms

Sample docker stacks for LaminDB.

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

Assembled Genomes Compressor

Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes

A pairwise sequence aligner written in Rust

A humble effort to expose datasets in a FAIR way using Schema.org and Bioschemas.org

your friendly pangenome graph genotyper