PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.
PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.
复制标题
DOI：
10.1111/2041-210x.12399
复制
发表时间：
2015-08
影响因子：
6.6
通讯作者：
Schonrogge K
中科院分区：
文献类型：
--
作者：
Gweon HS;Oliver A;Taylor J;Booth T;Gibbs M;Read DS;Griffiths RI;Schonrogge K
利用Illumina MiSeq测序平台生成的数据研究真菌生物多样性带来了许多生物信息学上的挑战，从质量过滤到生成已识别的操作分类单元（OTU）丰度表，每个分析步骤通常涉及大量工具。在这里，我们介绍PIPITS，一个开源的独立软件套件，用于自动处理Illumina MiSeq序列，用于真菌群落分析。PIPITS利用许多最先进的应用程序来处理从质量过滤到产生OTU丰度表的成对端读取。我们提供了管道的详细描述，并展示了它在分析Illumina MiSeq平台上生成的9 396 092序列中的实用性。PIPITS是第一个专门用于真菌ITS序列的自动化生物信息学管道，它结合ITSx提取ITS的子区域，并利用最新的RDP分类器对整理的UNITE真菌数据集进行序列分类。
Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables. Here, we introduce PIPITS, an open‐source stand‐alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired‐end reads from quality filtering to producing OTU abundance tables. We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.