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mettannotator:一个全面而可扩展的Nextflow注释管道,用于 prokaryotic 组件

Tatiana A Gurbich¹, Martin Beracochea¹, Nishadi H De Silva¹

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom.

Bioinformatics (Oxford, England)

|January 24, 2025

概括

Mettannotator是一个可扩展的Nextflow管道,用于注释原生生物基因组,包括新型物种. 它识别基因,预测功能,如抗菌素耐药性,并输出结果下游分析.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
微生物生态学微生物生态学

背景情况:

从分离物和环境样本中越来越多的 prokaryotic 基因组组合对注释提出了挑战.
在现有的参考数据库中,新物种的代表性往往很差,因此需要先进的注释工具.

研究的目的:

介绍mettaannotator,一个全面和可扩展的Nextflow管道用于 prokaryotic 基因组注释.
为了能够在规模上对已被详细描述的和新型的原生生物种类进行注释.

主要方法:

在Nextflow和Python中实现了Mettannotator管道.
它识别了编码和非编码区域,预测了蛋白质功能 (包括抗菌素耐药性),并划分了基因群.
结果总结在一个一般特征格式 (GFF) 文件中.

主要成果:

该管道在29个 prokaryotic phyla 的 200 个基因组上进行了测试,包括隔离基因组和元基因组组装基因组.
性能指标被生成并与其他注释工具进行比较.
该工具成功地注释了各种 prokaryotic 基因组,包括新 taxa.

结论:

Mettannotator为 prokaryotic 基因组注释提供了一个强大的和可扩展的解决方案.
该管道有助于下游分析和对基因组数据的可视化.
它解决了对已知和新型 prokaryotic 物种的有效注释的需求.

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