Comparing de novo genome assembly: the long and short of it.
Comparing de novo genome assembly: the long and short of it.
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DOI：
10.1371/journal.pone.0019175
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发表时间：
2011-04-29
期刊：
影响因子：
3.7
通讯作者：
Mishra B
中科院分区：
文献类型：
--
作者：
Narzisi G;Mishra B
DNA测序技术的最新进展及其在全基因组关联研究（GWAS）中的核心作用重新点燃了人们对全基因组序列组装（WGSA）问题日益增长的兴趣，从而使该领域充斥着大量新的形式化、算法、启发式和实现。然而，很少有人对这些装配器的质量和准确性进行比较评估。目前还没有普遍接受和标准化的比较方法。更糟糕的是，广泛用于比较组装序列的度量只强调大小，而不能很好地捕获组装质量和准确性。本文解决了这些问题：它通过对几个装配器的严格研究，在标准指标（N50，覆盖率，装配尺寸等）以及这里介绍的更全面的指标（特征响应曲线，FRC）下进行比较，突出了装配精度中的常见异常；FRC透明地捕获了组件的质量与大小之间的权衡。为此，对大多数公开可用的主要序列汇编器进行了比较，包括低覆盖长（Sanger）和高覆盖短（Illumina）读取技术。这些组装程序应用于微生物（大肠杆菌、布鲁氏菌、沃尔巴克氏菌、葡萄球菌、幽门螺杆菌）和部分人类基因组序列(Chr。Y)，使用不同的读取长度、覆盖范围、准确性以及有或没有配偶对的序列读取。我们希望，基于这些评估，计算生物学家将确定创新的序列组装范式，生物信息学家将确定开发“下一代”组装器的有希望的方法，生物技术学家将为测序技术平台制定更有意义的设计需求。一种新的计算FRC度量的软件工具已经开发出来，并可通过AMOS开源联盟获得。
Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium.
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