BamView: visualizing and interpretation of next-generation sequencing read alignments
BamView: visualizing and interpretation of next-generation sequencing read alignments
复制标题
DOI：
10.1093/bib/bbr073
复制
发表时间：
2013-03-01
影响因子：
9.5
通讯作者：
McQuillan, Jacqueline A.
中科院分区：
文献类型：
--
作者：
Carver, Tim;Harris, Simon R.;McQuillan, Jacqueline A.
所谓的下一代测序（NGS）提供了以低成本进行大规模测序的能力，使生物学家能够进行强大的实验并深入了解生物过程。 BamView 旨在可视化和分析来自 NGS 平台的序列读取，这些序列已与参考序列进行比对。它是一个桌面应用程序，用于浏览比对或映射的读数 [Ruffalo, M, LaFramboise, T, Koyuturk, M. 下一代测序读数比对算法的比较分析。 Bioinformatics 2011;27:2790-6] 在不同的放大水平下，从可以看到碱基质量的核苷酸水平，到显示总体覆盖度的基因组或染色体水平。为了深入研究 NGS 数据，提供了各种视图，可以配置这些视图来突出显示数据的有趣方面。可以叠加多个读取比对文件以比较不同实验的结果，并且可以应用过滤器来促进比对读取的解释。 BamView不仅是一个独立的应用程序，还可以用作Artemis基因组浏览器的集成部分，允许用户在参考基因组的序列和注释的背景下研究NGS数据。可以突出显示和研究单核苷酸多态性 (SNP) 密度和候选 SNP 位点，并且可以使用读对信息来发现大的结构插入和缺失。该应用程序还将计算读取映射的简单分析，包括报告用户选择的基因的读取计数和每千碱基每百万映射读取的读取（RPKM）。可用性：BamView和Artemis是免费提供的软件。这些可以从他们的主页下载：http://bamview.sourceforge.net/； http://www.sanger.ac.uk/resources/software/artemis/。要求：Java 1.6 或更高版本。
So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [ Ruffalo, M, LaFramboise, T, Koyuturk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user.Availability: BamView and Artemis are freely available software. These can be downloaded from their home pages: http://bamview.sourceforge.net/; http://www.sanger.ac.uk/resources/software/artemis/.Requirements: Java 1.6 or higher.