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

•We describe three long-read sequencing technologies and their characteristics.•We describe available algorithms for long-read assembly and their use.•Most microbial genomes can now be automatically finished using long reads.•The total cost of finishing microbial genomes is now under $1000.•New meth...

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Vydané v:Current opinion in microbiology Ročník 23; s. 110 - 120
Hlavní autori: Koren, Sergey, Phillippy, Adam M
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Elsevier Ltd 01.02.2015
Predmet:
automation
Chromosomes
Contig Mapping - methods
Contig Mapping - trends
genome
Genome, Microbial
Molecular Biology - methods
Molecular Biology - trends
Pathology
Sequence Analysis, DNA - methods
Sequence Analysis, DNA - trends
ISSN:1369-5274, 1879-0364, 1879-0364
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Popis
Shrnutí:•We describe three long-read sequencing technologies and their characteristics.•We describe available algorithms for long-read assembly and their use.•Most microbial genomes can now be automatically finished using long reads.•The total cost of finishing microbial genomes is now under $1000.•New methods are needed to assemble microbial populations and metagenomes. 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.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
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ObjectType-Review-3
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ISSN:1369-5274
1879-0364
1879-0364
DOI:10.1016/j.mib.2014.11.014