plasmidSPAdes: assembling plasmids from whole genome sequencing data

被引：379

作者：

Antipov, Dmitry ^{[1
]}

Hartwick, Nolan ^{[2
]}

Shen, Max ^{[3
]}

Raiko, Mikhail ^{[2
]}

Lapidus, Alla ^{[1
]}

Pevzner, Pavel A. ^{[1
,2
]}

机构：

[1] St Petersburg State Univ, Inst Translat Biomed, Ctr Algorithm Biotechnol, St Petersburg, Russia

[2] Univ Calif San Diego, Dept Comp Sci & Engn, San Diego, CA 92103 USA

[3] MIT, Bioinformat & Syst Biol Program, 77 Massachusetts Ave, Cambridge, MA 02139 USA

来源：

BIOINFORMATICS | 2016年 / 32卷 / 22期

关键词：

CLASSIFICATION;

D O I：

10.1093/bioinformatics/btw493

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. Results: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes.

引用

页码：3380 / 3387

页数：8

共 21 条

[1] Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome [J].

Anda, Mizue ;

Ohtsubo, Yoshiyuki ;

Okubo, Takashi ;

Sugawara, Masayuki ;

Nagata, Yuji ;

Tsuda, Masataka ;

Minamisawa, Kiwamu ;

Mitsui, Hisayuki .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (46) :14343-14347

[2] The RAST server: Rapid annotations using subsystems technology [J].

Aziz, Ramy K. ;

Bartels, Daniela ;

Best, Aaron A. ;

DeJongh, Matthew ;

Disz, Terrence ;

Edwards, Robert A. ;

Formsma, Kevin ;

Gerdes, Svetlana ;

Glass, Elizabeth M. ;

Kubal, Michael ;

Meyer, Folker ;

Olsen, Gary J. ;

Olson, Robert ;

Osterman, Andrei L. ;

Overbeek, Ross A. ;

McNeil, Leslie K. ;

Paarmann, Daniel ;

Paczian, Tobias ;

Parrello, Bruce ;

Pusch, Gordon D. ;

Reich, Claudia ;

Stevens, Rick ;

Vassieva, Olga ;

Vonstein, Veronika ;

Wilke, Andreas ;

Zagnitko, Olga .

BMC GENOMICS, 2008, 9 (1)

[3] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[4] In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing [J].

Carattoli, Alessandra ;

Zankari, Ea ;

Garcia-Fernandez, Aurora ;

Larsen, Mette Voldby ;

Lund, Ole ;

Villa, Laura ;

Aarestrup, Frank Moller ;

Hasman, Henrik .

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2014, 58 (07) :3895-3903

[5]

Compeau P., 2015, Bioinformatics Algorithms: An Active Learning Approach

[6] Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae [J].

Conlan, Sean ;

Thomas, Pamela J. ;

Deming, Clayton ;

Park, Morgan ;

Lau, Anna F. ;

Dekker, John P. ;

Snitkin, Evan S. ;

Clark, Tyson A. ;

Khai Luong ;

Song, Yi ;

Tsai, Yu-Chih ;

Boitano, Matthew ;

Dayal, Jyoti ;

Brooks, Shelise Y. ;

Schmidt, Brian ;

Young, Alice C. ;

Thomas, James W. ;

Bouffard, Gerard G. ;

Blakesley, Robert W. ;

Mullikin, James C. ;

Korlach, Jonas ;

Henderson, David K. ;

Frank, Karen M. ;

Palmore, Tara N. ;

Segre, Julia A. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (254)

[7] Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Escherichia coli Plasmids [J].

De Toro, Maria ;

Pilar Garcillan-Barcia, M. ;

De La Cruz, Fernando .

MICROBIOLOGY SPECTRUM, 2014, 2 (06)

[8] TRANSFORMATION OF SACCHAROMYCES-CEREVISIAE WITH LINEAR DNA KILLER PLASMIDS FROM KLUYVEROMYCES-LACTIS [J].

GUNGE, N ;

MURATA, K ;

SAKAGUCHI, K .

JOURNAL OF BACTERIOLOGY, 1982, 151 (01) :462-464

[9] QUAST: quality assessment tool for genome assemblies [J].

Gurevich, Alexey ;

Saveliev, Vladislav ;

Vyahhi, Nikolay ;

Tesler, Glenn .

BIOINFORMATICS, 2013, 29 (08) :1072-1075

[10] Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation [J].

Jackman, Shaun D. ;

Warren, Rene L. ;

Gibb, Ewan A. ;

Vandervalk, Benjamin P. ;

Mohamadi, Hamid ;

Chu, Justin ;

Raymond, Anthony ;

Pleasance, Stephen ;

Coope, Robin ;

Wildung, Mark R. ;

Ritland, Carol E. ;

Bousquet, Jean ;

Jones, Steven J. M. ;

Bohlmann, Joerg ;

Birol, Inanc .

GENOME BIOLOGY AND EVOLUTION, 2016, 8 (01) :29-41

← 1 2 3 →