Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
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DOI：
10.1186/1756-0500-4-149
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发表时间：
2011-05-26
影响因子：
1.8
通讯作者：
Klopp C
中科院分区：
文献类型：
--
作者：
Jérôme M;Noirot C;Klopp C
Roche 454 焦磷酸测序平台通常被认为是最通用的下一代测序技术平台，可以对大型基因组进行测序、变异分析或转录组研究。最近报道的一个偏差导致在一次运行中以随机方式对一个独特的 DNA 片段产生多次读取。这种偏差对使用读数测量片段表示的质量有直接影响。其他清洁步骤通常在组装或对齐之前对读数执行。 PyroCleaner 是一个软件模块，旨在清理 454 焦磷酸测序读数，以简化组装过程。该程序是一款免费软件，根据自由软件基金会发布的 GNU 通用公共许可证条款进行分发。它使用读重复、长度、复杂性、碱基对质量和未确定碱基数量等标准来实现多个过滤器。它还允许清理双端序列的流程图文件 (.sff)，一方面生成经过验证的双端文件，另一方面生成单个读取文件。读段清理一直是序列分析中的重要步骤。 pyrocleaner python模块是一把专用于454个reads清理的瑞士刀。它包括常用的过滤器以及专用过滤器，例如重复读取删除和双端读取验证。
Roche 454 pyrosequencing platform is often considered the most versatile of the Next Generation Sequencing technology platforms, permitting the sequencing of large genomes, the analysis of variations or the study of transcriptomes. A recent reported bias leads to the production of multiple reads for a unique DNA fragment in a random manner within a run. This bias has a direct impact on the quality of the measurement of the representation of the fragments using the reads. Other cleaning steps are usually performed on the reads before assembly or alignment. PyroCleaner is a software module intended to clean 454 pyrosequencing reads in order to ease the assembly process. This program is a free software and is distributed under the terms of the GNU General Public License as published by the Free Software Foundation. It implements several filters using criteria such as read duplication, length, complexity, base-pair quality and number of undetermined bases. It also permits to clean flowgram files (.sff) of paired-end sequences generating on one hand validated paired-ends file and the other hand single read file. Read cleaning has always been an important step in sequence analysis. The pyrocleaner python module is a Swiss knife dedicated to 454 reads cleaning. It includes commonly used filters as well as specialised ones such as duplicated read removal and paired-end read verification.