从 RNA-Seq 数据中检测 ncRNA 的管道基准测试。

A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data.

机构信息

Oncology, Nerviano Medical Sciences, Nerviano, Milan, Italy.

Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.

出版信息

Brief Bioinform. 2020 Dec 1;21(6):1987-1998. doi: 10.1093/bib/bbz110.

DOI:10.1093/bib/bbz110

PMID:31740918

Abstract

Next-Generation Sequencing (NGS) is a high-throughput technology widely applied to genome sequencing and transcriptome profiling. RNA-Seq uses NGS to reveal RNA identities and quantities in a given sample. However, it produces a huge amount of raw data that need to be preprocessed with fast and effective computational methods. RNA-Seq can look at different populations of RNAs, including ncRNAs. Indeed, in the last few years, several ncRNAs pipelines have been developed for ncRNAs analysis from RNA-Seq experiments. In this paper, we analyze eight recent pipelines (iSmaRT, iSRAP, miARma-Seq, Oasis 2, SPORTS1.0, sRNAnalyzer, sRNApipe, sRNA workbench) which allows the analysis not only of single specific classes of ncRNAs but also of more than one ncRNA classes. Our systematic performance evaluation aims at guiding users to select the appropriate pipeline for processing each ncRNA class, focusing on three key points: (i) accuracy in ncRNAs identification, (ii) accuracy in read count estimation and (iii) deployment and ease of use.

摘要

下一代测序（NGS）是一种高通量技术，广泛应用于基因组测序和转录组分析。RNA-Seq 使用 NGS 来揭示给定样本中 RNA 的身份和数量。然而，它会产生大量需要使用快速有效的计算方法进行预处理的原始数据。RNA-Seq 可以研究不同的 RNA 群体，包括 ncRNA。事实上，在过去几年中，已经开发了几个用于从 RNA-Seq 实验分析 ncRNA 的 ncRNA 管道。在本文中，我们分析了八个最近的管道（iSmaRT、iSRAP、miARma-Seq、Oasis 2、SPORTS1.0、sRNAnalyzer、sRNApipe、sRNA workbench），这些管道不仅可以分析单个特定类别的 ncRNA，还可以分析多个 ncRNA 类别。我们的系统性能评估旨在指导用户为处理每个 ncRNA 类别选择合适的管道，重点关注三个关键点：（i）ncRNA 识别的准确性，（ii）读段计数估计的准确性，以及（iii）部署和易用性。