SmashCell：用于分析单细胞扩增基因组序列的软件框架。
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
机构信息
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
出版信息
Bioinformatics. 2010 Dec 1;26(23):2979-80. doi: 10.1093/bioinformatics/btq564. Epub 2010 Oct 21.
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.
AVAILABILITY
The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
单细胞操作技术、全基因组扩增和高通量测序的最新进展使得对单个细胞的基因组进行测序成为可能。然而，这些基因组的生物信息学分析比使用传统基于培养的方法生成的基因组分析要复杂得多。为了简化分析，我们开发了 SmashCell（来自单细胞的简单宏基因组分析外壳）。它旨在以允许在每个步骤中探索参数和算法的方式自动化微生物基因组分析——组装、基因预测、功能注释的主要步骤。它还管理这些分析创建的数据，并提供可视化方法来快速分析结果。
可用性
SmashCell 的源代码和综合手册可在 http://asiago.stanford.edu/SmashCell 获得
联系人
补充信息
补充数据可在生物信息学在线获得。
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