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Curr Opin Microbiol. 2015 Feb;23:110-20. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1.

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

Author information

1
National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, United States.
2
National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, United States. Electronic address: phillippya@nbacc.net.

Abstract

Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes.

PMID:
25461581
DOI:
10.1016/j.mib.2014.11.014
[Indexed for MEDLINE]
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