Plaseval:比较和评估质粒检测工具的框架。

IF 2.9 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS
Aniket Mane, Haley Sanderson, Aaron P White, Rahat Zaheer, Robert Beiko, Cédric Chauve
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引用次数: 0

摘要

背景:质粒在细菌间通过水平基因转移传递抗菌药耐药性(AMR)基因方面发挥着重要作用。在短读组装中识别质粒是一个具有挑战性的问题,也是一个非常活跃的研究领域。质粒分选的目的是在基因组组装草案中检测可能来自同一质粒的等位基因组(bins)。最近开发了几种质粒分选方法,如 PlasBin-flow、HyAsP、gplas、MOB-suite 和 plasmidSPAdes。这就促使我们对质粒分选方法的性能进行评估,既可以根据给定的基本事实进行评估,也可以在两种方法之间进行评估:我们介绍了一种旨在比较质粒分选工具结果的新方法 PlasEval。PlasEval 计算两组质粒分选结果之间的不相似度,这两组质粒分选结果可以来自两个质粒分选工具,也可以来自一个质粒分选工具和一组质粒分选结果的基本真相。PlasEval 差异度考虑了质粒箱的等位基因内容、等位基因的长度,并具有重复感知功能。此外,PlasEval 计算出的不相似性得分被分解成几个部分,这样就能了解比较的质粒箱集之间的定性差异。我们通过对最近开发的四种质粒分选工具--PlasBin-flow、HyAsP、gplas 和 MOB-recon--在 53 个大肠杆菌基因组数据集上进行基准测试,来说明 PlasEval 的使用情况:结论:使用 PlasEval 对质粒分选方法的结果进行分析表明,这些方法的行为差异很大。PlasEval 可用来决定特定数据集应使用哪种特定的质粒分选方法。不同方法之间的分歧也表明,短读数等位基因的质粒分选问题需要进一步研究。我们相信,PlasEval 可以成为这方面的有效工具。PlasEval 可在 https://github.com/acme92/PlasEval 公开获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Plaseval: a framework for comparing and evaluating plasmid detection tools.

Background: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.

Results: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.

Conclusion: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.

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来源期刊
BMC Bioinformatics
BMC Bioinformatics 生物-生化研究方法
CiteScore
5.70
自引率
3.30%
发文量
506
审稿时长
4.3 months
期刊介绍: BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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