背景:泛病毒检测,一般的病毒检测,可能是具有挑战性的,主要是由于病毒中缺乏普遍保守的遗传元件。宏基因组下一代测序可以通过提供对微生物群落的无偏见概述,为这个问题提供有希望的解决方案。无需事先选择目标即可检测任何病毒。然而,利用宏基因组下一代测序进行病毒调查的一个主要挑战是数据分析可能非常复杂,涉及许多数据处理步骤。
结果:这里,我们介绍随行人员来应对这一挑战。Entourage支持短读取序列组装,使用基于重叠群的方法在有或没有参考病毒靶标的情况下进行病毒序列搜索,和样本内序列变异定量。Entourage中实现了多个工作流程,以便通过单个命令行进行端到端病毒序列检测分析,从阅读清洁,序列装配,病毒序列搜索。产生的结果是全面的,允许全面的质量控制,可靠性评估,和解释。我们通过使用Entourage来全面搜索目标病毒序列以及从掺入病毒的HeLa细胞培养样品中产生的原始序列读取数据,从而说明Entourage的实用程序作为病毒检测的简化工作流程。此外,我们通过分析预组装的TaraOceans数据集来展示其在现实世界数据集上的灵活性和性能。总的来说,我们的结果表明,即使在个位数的低病毒测序深度下,Entourage也表现良好,它可以有效地发现新病毒。此外,通过使用从患有慢性SARS-CoV-2感染的患者产生的序列数据,我们展示了Entourage量化病毒样片遗传变异的能力,并生成说明结果的出版物质量图。
结论:Entourage是多功能一体的,多才多艺,以及用于病毒调查的简化的生物信息学软件,开发的重点是易用性。根据MIT许可,Entourage可在https://codebug.org/CENMIG/Entourage获得。
BACKGROUND: Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps.
RESULTS: Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage\'s utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage\'s capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results.
CONCLUSIONS: Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.