Tate Alex J, Brown Kristen C, Montgomery Taiowa A
Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
Bioinform Adv. 2023 May 18;3(1):vbad065. doi: 10.1093/bioadv/vbad065. eCollection 2023.
tiny-count is a highly flexible counting tool that allows for hierarchical classification and quantification of small RNA reads from high-throughput sequencing data. Selection rules can be used to filter reads by 5' nucleotide, length, position of alignments in relation to reference features, and by the number of mismatches to reference sequences. tiny-count can quantify reads aligned to a genome or directly to small RNA or transcript sequences. With tiny-count, users can quantify a single class of small RNAs or multiple classes in parallel. tiny-count can resolve distinct classes of small RNAs, for example, piRNAs and siRNAs, produced from the same locus. It can distinguish small RNA variants, such as miRNAs and isomiRs, with single-nucleotide precision. tRNA, rRNA, and other RNA fragments can also be quantified. tiny-count can be run alone or as part of tinyRNA, a workflow that provides a basic all-in-one command line-based solution for small RNA-seq data analysis, with documentation and statistics generated at each step for accurate and reproducible results.
tiny-count and other tinyRNA tools are implemented in Python, C++, Cython, and R, and the workflow is coordinated with CWL. tiny-count and tinyRNA are free and open-source software distributed under the GPLv3 license. tiny-count can be installed via Bioconda (https://anaconda.org/bioconda/tiny-count) and both tiny-count and tinyRNA documentation and software downloads are available at https://github.com/MontgomeryLab/tinyRNA. Reference data, including genome and feature information, for certain species can be found at https://www.MontgomeryLab.org.
tiny-count是一种高度灵活的计数工具，可对来自高通量测序数据的小RNA读数进行分层分类和定量。选择规则可用于根据5'核苷酸、长度、与参考特征相关的比对位置以及与参考序列的错配数来过滤读数。tiny-count可以对与基因组比对的读数或直接与小RNA或转录本序列比对的读数进行定量。使用tiny-count，用户可以并行定量单一类别的小RNA或多类别小RNA。tiny-count可以解析从同一基因座产生的不同类别的小RNA，例如piRNA和siRNA。它可以以单核苷酸精度区分小RNA变体，如miRNA和isomiR。tRNA、rRNA和其他RNA片段也可以进行定量。tiny-count可以单独运行，也可以作为tinyRNA的一部分运行，tinyRNA是一个工作流程，为小RNA测序数据分析提供了一个基于命令行的基本一体化解决方案，在每个步骤都会生成文档和统计信息，以获得准确且可重复的结果。
tiny-count和其他tinyRNA工具用Python、C++、Cython和R实现，工作流程与CWL协调。tiny-count和tinyRNA是根据GPLv3许可分发的免费开源软件。tiny-count可以通过Bioconda（https://anaconda.org/bioconda/tiny-count）安装，tiny-count和tinyRNA的文档及软件下载可在https://github.com/MontgomeryLab/tinyRNA获取。某些物种的参考数据，包括基因组和特征信息，可在https://www.MontgomeryLab.org找到。
