ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis.
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis.
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DOI：
10.12688/f1000research.15704.1
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发表时间：
2018
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影响因子：
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通讯作者：
Armstrong SD
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文献类型：
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作者：
Rivers AR;Weber KC;Gardner TG;Liu S;Armstrong SD
小亚基核糖体RNA基因和大亚基核糖体RNA基因之间的内部转录间隔区（ITS）是真菌和其他分类群广泛使用的系统发育标记。真核ITS含有保守的5.8S rRNA，分为ITS1和ITS2高变区。这些区域在长度上是可变的，并且使用与它们的侧翼基因的保守区域互补的引物进行扩增。先前的研究表明，去除保守区域可以获得更准确的分类。现有的软件程序ITSx能够通过使用软件套件HMMER将隐藏马尔可夫模型剖面与保守基因的末端匹配来修剪FASTA序列。ITSxpress的开发是为了将该技术从使用操作分类单位（OTU）的标记基因研究扩展到使用精确序列变体的研究；Dada2、Deblur、QIIME 2、Unoise等软件包使用的方法。序列变体方法使用每次读取的质量分数来识别统计上可能代表真实序列的序列。itsexpress通过处理FASTQ而不是FASTA文件来实现这一点。该软件还通过临时聚类在扩增子数据中常见的高度相似的序列并利用优化的Hmmsearch参数，在4核计算机上将读取的修剪速度提高了14-23倍。ITSxpress是一个QIIME 2插件，也是一个独立的应用程序，可以从Python包索引、Bioconda和Github安装。
The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.