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