SmashCell: A software framework for the analysis of single-cell amplified genome sequences.

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

SmashCell: A software framework for the analysis of single-cell amplified genome sequences. / Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen; Bork, Peer; Relman, David a.

In: Bioinformatics, Vol. 26, No. 23, 10.2010, p. 2979-2980.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Harrington, ED, Arumugam, M, Raes, J, Bork, P & Relman, DA 2010, 'SmashCell: A software framework for the analysis of single-cell amplified genome sequences.', Bioinformatics, vol. 26, no. 23, pp. 2979-2980. https://doi.org/10.1093/bioinformatics/btq564

APA

Harrington, E. D., Arumugam, M., Raes, J., Bork, P., & Relman, D. A. (2010). SmashCell: A software framework for the analysis of single-cell amplified genome sequences. Bioinformatics, 26(23), 2979-2980. https://doi.org/10.1093/bioinformatics/btq564

Vancouver

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA. SmashCell: A software framework for the analysis of single-cell amplified genome sequences. Bioinformatics. 2010 Oct;26(23):2979-2980. https://doi.org/10.1093/bioinformatics/btq564

Author

Harrington, Eoghan D ; Arumugam, Manimozhiyan ; Raes, Jeroen ; Bork, Peer ; Relman, David a. / SmashCell: A software framework for the analysis of single-cell amplified genome sequences. In: Bioinformatics. 2010 ; Vol. 26, No. 23. pp. 2979-2980.

Bibtex

@article{72297dfb496e46aba7386cb55d5a4e28,
title = "SmashCell: A software framework for the analysis of single-cell amplified genome sequences.",
abstract = "SUMMARY: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes however is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis - assembly, gene prediction, functional annotation - in a way that allows parameter and algorithm exploration at each step in the process. It alsomanages the data created by these analyses and provides visualisation methods to allow rapid analysis of the results. AVAILABILITY: The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell CONTACT: eoghanh@stanford.edu.",
author = "Harrington, {Eoghan D} and Manimozhiyan Arumugam and Jeroen Raes and Peer Bork and Relman, {David a}",
year = "2010",
month = oct,
doi = "10.1093/bioinformatics/btq564",
language = "English",
volume = "26",
pages = "2979--2980",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "23",

}

RIS

TY - JOUR

T1 - SmashCell: A software framework for the analysis of single-cell amplified genome sequences.

AU - Harrington, Eoghan D

AU - Arumugam, Manimozhiyan

AU - Raes, Jeroen

AU - Bork, Peer

AU - Relman, David a

PY - 2010/10

Y1 - 2010/10

N2 - SUMMARY: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes however is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis - assembly, gene prediction, functional annotation - in a way that allows parameter and algorithm exploration at each step in the process. It alsomanages the data created by these analyses and provides visualisation methods to allow rapid analysis of the results. AVAILABILITY: The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell CONTACT: eoghanh@stanford.edu.

AB - SUMMARY: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes however is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis - assembly, gene prediction, functional annotation - in a way that allows parameter and algorithm exploration at each step in the process. It alsomanages the data created by these analyses and provides visualisation methods to allow rapid analysis of the results. AVAILABILITY: The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell CONTACT: eoghanh@stanford.edu.

U2 - 10.1093/bioinformatics/btq564

DO - 10.1093/bioinformatics/btq564

M3 - Journal article

C2 - 20966005

VL - 26

SP - 2979

EP - 2980

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 23

ER -

ID: 43976281