BIGpre: a quality assessment package for next-generation sequencing data.
BIGpre: a quality assessment package for next-generation sequencing data.
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DOI：
10.1016/s1672-0229(11)60027-2
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发表时间：
2011-12
期刊：
影响因子：
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通讯作者：
Hu S
中科院分区：
文献类型：
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作者：
Zhang T;Luo Y;Liu K;Pan L;Zhang B;Yu J;Hu S
下一代测序(NGS)技术的出现显著提高了测序吞吐量，降低了成本。然而，短的读取长度、重复读取和海量的数据量使得数据处理比第一代测序技术更加困难和复杂。尽管已经开发了一些软件包来评估数据质量，但这些软件包要么对用户来说不容易获得，要么需要生物信息学技能和计算机资源。而且，目前几乎所有的质量评估软件在处理NGS数据中的重复评估时，都没有考虑到排序误差。在这里，我们介绍了一个新的用户友好的质量评估软件包BIGpre，它可以在Illumina和454平台上运行。BIGpre包含了其他质量评估软件的所有功能，如正向和反向读取之间的关联、读取GC-内容分布和基本NS质量。更重要的是，BIGpre结合了相关的程序来检测和删除重复读取，在考虑到排序错误并从原始数据中修剪低质量读取之后。BIGpre主要是用Perl编写的，并集成了统计程序包R中的图形功能。该程序包为来自Illumina和454平台的数据集排序生成表格和图形数据质量摘要。该软件包在几分钟内处理数亿次读取，为用户提供即时诊断信息，以便用户为下游分析操作测序数据。BIGPRE可在http://bigpre.sourceforge.net/.上免费获得
The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn’t taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net/.