An optimized strategy for genome assembly of Sanger/pyrosequencing hybrid data using available software

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Title
An optimized strategy for genome assembly of Sanger/pyrosequencing hybrid data using available software
Author(s)
Haeyoung Jeong; Jihyun Kim
Bibliographic Citation
Genomics & Informatics, vol. 6, no. 2, pp. 87-90
Publication Year
2008
Abstract
During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platformderived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.
Keyword
hybrid assemblypyrosequencingresequencing
ISSN
I000-0158
Publisher
Korea Soc-Assoc-Inst
DOI
http://dx.doi.org/10.5808/GI.2008.6.2.087
Type
Article
Appears in Collections:
Division of Research on National Challenges > Infectious Disease Research Center > 1. Journal Articles
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