Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland.
Department of Virology, University of Helsinki, 00014, Helsinki, Finland.
BMC Bioinformatics. 2022 May 28;23(1):196. doi: 10.1186/s12859-022-04709-8.
SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in-depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance.
Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high-level functionalities including lineage assignment, outlier filtering, aligning, phylogenetic tree reconstruction, cluster extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland with the main emphasis on fast screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations.
ClusTRace provides an effective interface that can significantly cut down learning and operating costs related to complex bioinformatic analysis of large viral sequence sets and phylogenies. All code is freely available from https://bitbucket.org/plyusnin/clustrace/.
自 2019 年 12 月以来，SARS-CoV-2 是高传染性的 2019 年冠状病毒病（COVID-19）的病原体，已成为全球科学和公共卫生的挑战。SARS-CoV-2 已经在全球范围内出现了几种新的变体，这引起了人们对 COVID-19 预防和治疗的关注。因此，及早发现和深入分析新出现的变体，以便预先发出警报和采取缓解措施至关重要。
在这里，我们提出了 ClusTRace，这是一种用于快速分析大型病毒系统发育中序列簇或分支的新型生物信息学管道。ClusTRace 提供了几个高级功能，包括谱系分配、异常值过滤、对齐、系统发育树重建、簇提取、变体调用、可视化和报告。ClusTRace 是作为芬兰 COVID-19 传播链追踪的辅助工具开发的，主要侧重于快速筛选系统发育，以寻找超级传播事件的标志物和其他关注点，例如簇增长速度快和/或新突变积累。
ClusTRace 提供了一个有效的接口，可以大大降低与分析大型病毒序列集和系统发育相关的复杂生物信息学的学习和运营成本。所有代码均可从 https://bitbucket.org/plyusnin/clustrace/ 免费获得。
