ReadXplorer——比对序列的可视化与分析
ReadXplorer--visualization and analysis of mapped sequences.
作者信息
Hilker Rolf, Stadermann Kai Bernd, Doppmeier Daniel, Kalinowski Jörn, Stoye Jens, Straube Jasmin, Winnebald Jörn, Goesmann Alexander
机构信息
Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany.
Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, GermanyInstitute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany.
出版信息
Bioinformatics. 2014 Aug 15;30(16):2247-54. doi: 10.1093/bioinformatics/btu205. Epub 2014 Apr 30.
MOTIVATION
Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data.
RESULTS
ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion-insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets.
AVAILABILITY AND IMPLEMENTATION
ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual.
动机
对于日益增长的基因组和转录组下一代测序数据进行全面分析，需要快速算法和精心安排的可视化。
结果
ReadXplorer是一款软件，为映射到参考序列上的基因组和转录组DNA序列提供直观的可视化和广泛的分析功能。ReadXplorer的一个独特之处在于读取映射的质量分类。它被纳入所有分析功能，并显示在ReadXplorer的各种同步数据查看器中，用于（i）参考序列、其碱基覆盖情况，以（ii）可归一化图和（iii）直方图、（iv）读取比对以及（v）读取对的形式呈现。ReadXplorer的分析能力涵盖RNA二级结构预测、单核苷酸多态性和缺失插入多态性检测、基因组特征和一般覆盖分析。特别是对于RNA-Seq数据，它提供差异基因表达分析、转录起始位点和操纵子检测以及RPKM值和读取计数计算。此外，ReadXplorer可以合并或叠加不同数据集的覆盖情况。
可用性和实现方式
ReadXplorer作为开源软件可在http://www.readxplorer.org获取，并附带详细手册。
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