Sergey Koren, PhD

Associate Investigator

Sergey received his PhD in computer science in 2012 under the supervision of Mihai Pop at the University of Maryland. He joined the National Bioforensics Analysis Center in 2011 and was appointed as an associate principal investigator in 2014. During this time, he pioneered the use of single-molecule sequencing for the reconstruction of complete genomes. In 2015, he joined the National Human Genome Research Institute as a founding member of the Genome Informatics Section. His research focuses on the efficient analysis of large-scale genomic datasets and new methods for metagenomic analysis and assembly of high-noise single-molecule sequencing data.



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.


Evaluate genome assemblies with k-mers and more


A long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.


Long-read metagenomic analysis
News posts

Human genome assemblies with nanopore, an update

May 23, 2018

Assembling the Cliveome

April 28, 2017

Assembly of a human genome from nanopore sequencing data

January 8, 2017
The reference genome of Macropodus opercularis (the paradise fish)
Scientific Data, May 25, 2024
Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Nature Methods, May 10, 2024
Cheng H, Asri M, Lucas J, Koren S, Li H
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Genome Research, April 16, 2024
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga JM, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B