zoukankan      html  css  js  c++  java
  • Fast and accurate de novo genome assembly from long uncorrected reads

    Fast and accurate de novo genome assembly from long uncorrected reads

    快速和准确的从头基因组组装从长时间未纠正的read

    1. Robert Vaser1,5
    2. Ivan Sović2,5
    3. Niranjan Nagarajan3 and 
    4. Mile Šikić1,4

    +Author Affiliations

    1. 1Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, 10000 Zagreb, Croatia;
    2. 2Centre for Informatics and Computing, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
    3. 3Genome Institute of Singapore, Singapore 138672, Singapore;
    4. 4Bioinformatics Institute, Singapore 138671, Singapore
    1. Corresponding author: mile.sikic@fer.hr
    1. 5 These authors contributed equally to this work.

    Abstract

    The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment–based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

    太平洋生物科学公司和牛津纳米孔技术公司的长片段组装通常需要资源密集型的纠错和共识生成步骤,以获得高质量的组装。
    我们的研究表明,使用名为Racon的simd加速、基于部分顺序对齐的独立的consensus模块,可以省去错误校正步骤,并有效地生成高质量的consensus序列。
    基于对PacBio和Oxford Nanopore数据集的测试,我们发现,Racon与miniasm相结合可以实现与最先进的方法相似或更好的一致基因组,同时速度更快一个数量级。

  • 相关阅读:
    利用Hexo搭建个人博客-环境搭建篇
    Appium的安装-MAC平台
    alias指令:设置命令别名
    Android学习——第一个NDK程序
    Android学习——windows下搭建Cygwin环境
    Android学习——windows下搭建NDK_r9环境
    Win7&Ubuntu12.04 双系统引导问题
    Android学习第三天-签名常用命令
    Android学习第三天-打包常用命令
    Android学习第二天-android常用命令
  • 原文地址:https://www.cnblogs.com/wangprince2017/p/13756517.html
Copyright © 2011-2022 走看看