Introduction

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.The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCelleoghanh@stanford.eduSupplementary data are available at Bioinformatics online.

Publications

  1. SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
    Cite this
    Harrington ED, Arumugam M, Raes J, Bork P, Relman DA, 2010-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Eoghan D Harrington
    Developer

    Department of Microbiology and Immunology, Stanford University School of Medicine, United States of America

  2. Manimozhiyan Arumugam
    Developer

  3. Jeroen Raes
    Developer

  4. Peer Bork
    Developer

  5. David A Relman
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006360
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByDavid A Relman