Short read fragment assembly of bacterial genomes.

TitleShort read fragment assembly of bacterial genomes.
Publication TypeJournal Article
Year of Publication2008
AuthorsChaisson MJ, Pevzner PA
JournalGenome Res
Volume18
Issue2
Pagination324-30
Date Published2008 Feb
ISSN1088-9051
KeywordsAlgorithms, Contig Mapping, Genome, Bacterial, Genomics, Research Design, Sequence Analysis, DNA
Abstract

In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.

DOI10.1101/gr.7088808
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18083777?dopt=Abstract
PMCPMC2203630
Alternate TitleGenome Res.
PubMed ID18083777