Seminar One-step Bacterial Genome Closure with Single-molecule Hybrid Assembly

Talk Title:

One-step Bacterial Genome Closure with Single-molecule Hybrid Assembly


Emerging single-molecule sequencing instruments can generate multi-kilobase sequences with the potential to dramatically improve genome and transcriptome assembly. However, the high error rate of single-molecule reads is challenging, and has limited their use to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that utilizes shorter, high identity sequences to correct the error in single-molecule sequences. We present an assembly recipe combining long high-error sequences and short high-idenitity sequences that can generate near-finished bacterial genomes. We demonstrate the utility of this approach on several bacterial genomes: in the best examples, producing automatically closed bacterial chromosomes without the use of paired ends.


Sergey Koren, Ph.D.

Bioinformatics Scientist, Genomics

National Biodefense Analysis and Countermeasures Center


Center for Bioinformatics and Computational Biology

University of Maryland

Email: sergek

Reference Publication:

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, and Phillippy AM.

Nature Biotechnology 30(7):693-700 2012

Location and Time: 4202 GBSF 11am-12pm Thursday, November 15th

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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