Sergey Koren, PhD
Research Professor
jhu.edu
Sergey is a Research Professor in the Department of Computer Science at the Johns Hopkins University. His research focuses on the efficient analysis of large-scale genomic datasets and new methods for analysis and assembly of high-noise single-molecule sequencing data. 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.
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.
GQC (Genome Quality Checker)
GQC is a benchmarking tool for evaluating sequence reads and assemblies against a genome benchmark.
TTT
Trivial Tangle Traverser (TTT) is a tool developed to construct model sequences for the remaining gaps in the T2T assemblies and replace error-prone and labour-intensive manual graph curation step.
Verkko-Fillet
Post-verkko graph and assembly curation in Python
News posts
Verkko2 is released!
January 2, 2025Human genome assemblies with nanopore, an update
May 23, 2018Assembling the Cliveome
April 28, 2017Assembly of a human genome from nanopore sequencing data
January 8, 2017
Publications