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

Eoghan D Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David a Relman

doi:10.1093/bioinformatics/btq564

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

Eoghan D Harrington, Manimozhiyan Arumugam, Jeroen Raes, Peer Bork, David a Relman

12 Citations (Scopus)

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 also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.

Original language	English
Journal	Bioinformatics
Volume	26
Issue number	23
Pages (from-to)	2979-2980
Number of pages	2
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btq564
Publication status	Published - Dec 2010

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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 also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.",

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AU - Harrington, Eoghan D

AU - Arumugam, Manimozhiyan

AU - Raes, Jeroen

AU - Bork, Peer

AU - Relman, David a

PY - 2010/12

Y1 - 2010/12

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 also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.

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 also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.

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JO - Bioinformatics

JF - Bioinformatics

IS - 23

ER -

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

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