doi: 10.1038/nbt.1966
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Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
Hamidreza Chitsaz, Joyclyn L Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L Dupont, Jonathan H Badger, Mark Novotny, Douglas B Rusch, Louise J Fraser, Niall A Gormley, Ole Schulz-Trieglaff, Geoffrey P Smith, Dirk J Evers, Pavel A Pevzner & Roger S Lasken
Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single Escherichia coli and Staphylococcus aureus cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many E. coli cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.
doi: 10.1089/cmb.2012.0021
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich,1,2 Sergey Nurk,1,2 Dmitry Antipov,1 Alexey A. Gurevich,1 Mikhail Dvorkin,1 Alexander S. Kulikov,1,3 Valery M. Lesin,1 Sergey I. Nikolenko,1,3 Son Pham,4 Andrey D. Prjibelski,1 Alexey V. Pyshkin,1 Alexander V. Sirotkin,1 Nikolay Vyahhi,1 Glenn Tesler,5 Max A. Alekseyev,1,6 and Pavel A. Pevzner
The lions share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.
来源：生物谷
摘自网址：http://www.360zhyx.com/home-research-index-rid-26070.shtml
