Simon Heumos

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

The paper introduces nf-core/pangenome, a scalable and reference-unbiased pipeline for constructing pangenome graphs, achieving faster performance than PGGB on large datasets.

The paper introduces nf-core/airrflow, a Nextflow-based workflow for processing AIRR-seq data, validated on simulated and real datasets to analyze immune receptor repertoires.

This paper introduces a graph layout algorithm for pangenome graphs, enabling efficient visualization of large-scale genomic data.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

ODGI is a tool suite for analyzing pangenome graphs, enabling efficient exploration and manipulation of large-scale genomic data.

The paper introduces two C++ libraries for efficient manipulation of pangenomic graphs, showing improved performance over existing tools.