Helmholtz Gemeinschaft

Search
Browse
Statistics
Feeds

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

Item Type:Article
Title:SmashCell: a software framework for the analysis of single-cell amplified genome sequences
Creators Name:Harrington, E.D. and Arumugam, M. and Raes, J. and Bork, P. and Relman, D.A.
Abstract: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.
Keywords:Algorithms, Chromosome Mapping, DNA Sequence Analysis, Genome, Genomics, Nucleic Acid Amplification Techniques, Single-Cell Analysis, Software
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford University Press (U.K.)
Volume:26
Number:23
Page Range:2979-2980
Date:1 December 2010
Official Publication:https://doi.org/10.1093/bioinformatics/btq564
PubMed:View item in PubMed

Repository Staff Only: item control page

Open Access
MDC Library