A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads

一种基于序列的新方法，用于评价第三代测序Reads的质量

作者:

Wenjing Zhang,Neng Huang,Jiantao Zheng,Xingyu Liao,Jianxin Wang,Hong-Dong Li

作者背景:

School of Information Science and Engineering, Central South University, Changsha 410083, China; wjzhang@csu.edu.cn (W.Z.); huangneng@csu.edu.cn (N.H.); jiantao@csu.edu.cn (J.Z.); liaoxingyu@csu.edu.cn (X.L.); jxwang@csu.edu.cn (J.W.)

DOI:10.3390/genes10010044

文章关键词:Genomics,Read quality assessment,Third-generation sequencing

原文摘要:The advent of third-generation sequencing (TGS) technologies, such as the Pacific Biosciences (PacBio) and Oxford Nanopore machines, provides new possibilities for contig assembly, scaffolding, and high-performance computing in bioinformatics due to its long reads. However, the high error rate and poor quality of TGS reads provide new challenges for accurate genome assembly and long-read alignment. Efficient processing methods are in need to prioritize high-quality reads for improving the results of error correction and assembly. In this study, we proposed a novel Read Quality Evaluation and Selection Tool (REQUEST) for evaluating the quality of third-generation long reads. REQUEST generates training data of high-quality and low-quality reads which are characterized by their nucleotide combinations. A linear regression model was built to score the quality of reads. The method was tested on three datasets of different species. The results showed that the top-scored reads prioritized by REQUEST achieved higher alignment accuracies. The contig assembly results based on the top-scored reads also outperformed conventional approaches that use all reads. REQUEST is able to distinguish high-quality reads from low-quality ones without using reference genomes, making it a promising alternative sequence-quality evaluation method to alignment-based algorithms.

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads相关推荐

Developing a new mesh quality evaluation method based on convolutional neural network——方向1笔记
方向一:网格质量的评估基于卷积神经网络的网格质量评价方法研究(Developing a new mesh quality evaluation method based on convolution ...
《2006_ICPR_Low Resolution Character Recognition by Image Quality Evaluation》阅读笔记
论文主要思想这是一篇关于低质量字符图像识别的文章,这里的"低质量"指的是字符图像的分辨率低. 作者在文中指出,传统的(指的是2006年之前)低质量字符图像识别方法主要分为两类:第 ...
LLMs之Vicuna：《Vicuna: An Open-Source Chatbot Impressing GPT-4 with 90%* ChatGPT Quality》翻译与解读
LLMs之Vicuna:<Vicuna: An Open-Source Chatbot Impressing GPT-4 with 90%* ChatGPT Quality>翻译与解读导 ...
A Survey for Image Quality Assessment（综述）
图像质量评价相关内容总结,旨在回顾近二十年来的发展历程,供参考. 一.主观图像质量评价 (1) 主观图像质量评价实验:absolute category rating.pair comparison ...
Quality Assessment Paper List（研二）
从2018年5月到2019年5月,大概一年(研二)的时间里学习的有关quality assessment的论文.(共128篇) <PS:红色标注为经典论文> 相关代码可以在以下百度云盘链接 ...
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads 混合和非混合方法对nanopore ...
【论文review+总结】屏幕内容图像质量评估SC-IQA（Screen Content Image Quality Assessment）
目录论文review 2017年论文 2018年论文 2019年论文总结主要思路主要方法总结全参考FR-IQA 弱参考RR-IQA 无参考NR-IQA 多内容(不只局限于SCIs--基于cr ...
【演化计算】【论文研读】Completely Automated CNN Architecture Design Based on Blocks
Completely Automated CNN Architecture Design Based on Blocks 论文研读 I. INTRODUCTION II. BACKGROUND A. ...
视频主观质量评价工具：MSU Perceptual Video Quality tool
MSU Perceptual Video Quality tool是莫斯科国立大学(Moscow State University)的Graphics and Media Lab制作的一款视频主观评价 ...

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads相关推荐

最新文章

热门文章