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miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline
bioRxiv - Bioinformatics Pub Date : 2021-01-19 , DOI: 10.1101/2021.01.18.427129
Arun H. Patil , Marc K. Halushka

MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. Our laboratory previously developed miRge and miRge2.0, as flexible tools to process sequencing data for annotation of miRNAs and other small-RNA species and further predict novel miRNAs using a support vector machine approach. Although, miRge2.0 is a leading analysis tool in terms of speed with unique quantifying and annotation features, it has a few limitations. We present miRge3.0 which provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets and an accurate GFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. Finally, miRge3.0 output integrates into other packages for a streamlined analysis process and provides a cross-platform Graphical User Interface (GUI). In conclusion miRge3.0 is our 3rd generation small RNA-seq aligner with improvements in speed, versatility, and functionality over earlier iterations.

中文翻译:

miRge3.0:全面的microRNA和tRF测序分析流程

MicroRNA和tRF是一类小的非编码RNA,因其在基因的翻译调控中的作用而闻名。下一代测序(NGS)的进步已经实现了高通量的小RNA序列研究,这需要强大的比对管道。我们的实验室先前开发了miRge和miRge2.0,作为处理测序数据的灵活工具,用于注释miRNA和其他小RNA种类,并使用支持向量机方法进一步预测新型miRNA。尽管就速度而言,miRge2.0是领先的分析工具,具有独特的量化和注释功能,但它仍有一些局限性。我们展示了miRge3.0,它提供了更多功能以及与Cutadapt和Python的较新版本的兼容性。该工具的修订版包括处理唯一分子标识符(UMI)以在定量数据集中的miRNA时说明PCR重复的能力,以及精确的GFF3格式的isomiR工具。miRge3.0还具有以miRge2.0,Chimira和sRNAbench为基准的速度改进。最后,miRge3.0输出集成到其他软件包中以简化分析过程,并提供跨平台的图形用户界面(GUI)。总之,miRge3.0是我们的第三代小型RNA序列比对仪,与早期迭代相比,其速度,多功能性和功能得到了改善。0输出集成到其他程序包中以简化分析过程,并提供跨平台的图形用户界面(GUI)。总之,miRge3.0是我们的第三代小型RNA序列比对仪,与早期迭代相比,其速度,多功能性和功能得到了改善。0输出集成到其他程序包中以简化分析过程,并提供跨平台的图形用户界面(GUI)。总之,miRge3.0是我们的第三代小型RNA序列比对仪,与早期迭代相比,其速度,多功能性和功能得到了改善。
更新日期:2021-01-20
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