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

Filling the holes in whole genomes

August 6, 2026

For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium published a special collection of 12 papers in Cell and Cell Genomics heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders).

We're moving!

April 19, 2026

Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed one hour north on I-95 to set up shop at Johns Hopkins University. This is a very bittersweet move for me, as NHGRI has provided an incredibly supportive environment for my research, both in terms of colleagues and resources, and it’s hard to say goodbye. However, I am excited for the opportunity to tackle some new challenges at JHU.

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fun to chat with and I was in a slightly opinionated mood from the start — “The idea of a single reference genome is outdated,” says NIH researcher Adam Phillippy.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.

Publications
Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere
Cell, August 6, 2026
Phillippy AM, Mao Y, Kang Y, Šikić M, Miga KH
Telomere-to-telomere genome assembly and a pangenome for the rat
Cell Genomics, August 6, 2026
Li K, Ciosek JL, Koren S, Phillippy AM, Zhu Y, Lauer WA, Brooks SY, Bouffard GG, Pickett BD, Dumont BL, Smith ML, Kalbfleisch TS, Doris PA
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 for scalability to visualizae large tandem repeats across whole chromosomes.