Pavel A. Pevzner

Assembly of long, error-prone reads using repeat graphs

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most ...

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell gen...

An Eulerian path approach to DNA fragment assembly

For the last 20 years, fragment assembly in DNA sequencing followed the “overlap–layout–consensus” paradigm that is used in all currently available assembly tools. Although this...

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

How to apply de Bruijn graphs to genome assembly

Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution

Fragment assembly with short reads

Abstract Motivation: Current DNA sequencing technology produces reads of about 500–750 bp, with typical coverage under 10×. New sequencing technologies are emerging that produce...

Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitation...

Colored de Bruijn Graphs and the Genome Halving Problem

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, t...

SEQuel: improving the accuracy of genome assemblies

Abstract Motivation: Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the ass...

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Abstract Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequen...

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes

Recent analysis of genome rearrangements in human and mouse genomes revealed evidence for more rearrangements than thought previously and shed light on previously unknown featur...