StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies
StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies
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DOI：
10.1111/1755-0998.12187
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发表时间：
2014-03-01
影响因子：
7.7
通讯作者：
Mengoni, A.
中科院分区：
文献类型：
--
作者：
Bacci, G.;Bazzicalupo, M.;Mengoni, A.
新一代测序技术被广泛应用于分子微生物生态学领域，用于描述微生物群落的分类组成和推断微生物群落的功能。特别是基于PCR扩增子文库测序的所谓条形码或元遗传应用目前非常流行。其中一个与这些文库数据的利用相关的问题是分析reads质量和去除（修剪）低质量片段，同时为后续分析（例如分类分配）保留足够的信息。在这里，我们展示StreamingTrim，一个用Java编写的DNA读取修剪软件，研究人员可以用它来分析快速文件中DNA序列的质量，并以非常保守的方式搜索低质量区域。该软件开发的目的是提供一种工具，能够修剪扩增子库数据，保留尽可能多的分类信息。本软件配有图形用户界面，方便用户使用。此外，从计算的角度来看，StreamingTrim从输入fastq文件中逐一读取和分析序列，而不需要在内存中保留任何内容，从而允许在普通台式PC甚至笔记本电脑上运行计算。裁剪后的序列保存在输出文件中，并显示统计摘要，其中包含整个序列文件的长度和质量的平均值和标准差。编译后的软件、手册和示例数据集可以在GitHub存储库的BSD-2-Clause许可下获得。
Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at .