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

Talk Title:

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

Abstract:

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.

Speaker:

Sergey Koren, Ph.D.

Bioinformatics Scientist, Genomics

National Biodefense Analysis and Countermeasures Center

Affiliations:

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

http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2280.html

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 View all posts by Jonathan Eisen