Genome Informatics Section

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

People
News

Choose your reference wisely

October 13, 2025

In honor of ASHG week, see “Choose your human genome reference wisely”(no paywall), in which Vivien Marx interviewed me on the state of the human reference genome. Vivien is always fun to chat with and I was in a slightly opinionated mood from the start — “The idea of a single reference genome is outdated,” says NIH researcher Adam Phillippy. Some of my other quotes follow with a little added context.

The formation and propagation of human Robertsonian chromosomes

September 24, 2025

🚂 The T2T train keeps rolling. Our latest work investigating the structure and cause of Robertsonian chromosomes with the Gerton and Garrison labs is out today in the journal Nature! What’s a Robertsonian chromosome and why do they matter? More info below the break…

The Q100 preprint!

September 22, 2025

We are delighted to finally announce a preprint describing the Q100 project, where we finished the HG002 genome to near-perfect accuracy: A complete diploid human genome benchmark for personalized genomics

Publications
Reference-guided assembly of metagenomes with MetaCompass
Cell Reports Methods, September 26, 2025
Luan T, Cepeda-Espinoza VP, Liu B, Bowen Z, Ayyangar U, Almeida M, Koren S, Treangen TJ, Porter A, Pop M
Software

Verkko

Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.

Mash

Fast genome and metagenome distance and containment estimation using MinHash

Krona

Interactively explore metagenomes and more from a web browser

Merqury

Evaluate genome assemblies with k-mers and more

ModDotPlot

ModDotPlot is a dotplot visualization tool, built to quickly visualize large complex repeats within whole chromosomes.