BACKGROUND The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses. FINDINGS We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance-, 16S ribosomal RNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and we show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks. CONCLUSIONS While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software package to reliably assign taxon labels to microbial genomes. CAMITAX is available under Apache License 2.0 at https://github.com/CAMI-challenge/CAMITAX.

中文翻译：

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CAMITAX：微生物基因组的分类群标签。

背景技术微生物基因组序列的数量呈指数增长，特别是由于从元基因组和单细胞中回收完整或接近完整的基因组的最新进展。为基因组分配可靠的分类单元标签是关键，并且通常是进行下游分析的先决条件。结果我们介绍了CAMITAX，这是一种可扩展且可重现的工作流程，用于对从分离株，单细胞和元基因组中回收的微生物基因组进行分类标记。CAMITAX将基因组距离，16S核糖体RNA基因和基于基因同源性的分类分配与系统发生位置相结合。它使用Nextflow来编排参考数据库和软件容器，从而将安装和使用的便利性与计算的可重复性结合在一起。我们对来自TARA Oceans项目的具有高质量分类注释的数百个由基因组组装的基因组进行了评估，结果表明CAMITAX中的集成分类方法在测试等级上的所有单独方法上均得到了改进。结论当我们最初开发CAMITAX来帮助进行元基因组解释的关键评估（CAMI）计划时，它演变成一个综合软件包，可以可靠地将分类群标签分配给微生物基因组。CAMITAX可通过Apache License 2.0获得，网址为https://github.com/CAMI-challenge/CAMITAX。结论当我们最初开发CAMITAX来帮助进行元基因组解释的关键评估（CAMI）计划时，它演变成一个综合软件包，可以可靠地将分类群标签分配给微生物基因组。CAMITAX可通过Apache License 2.0获得，网址为https://github.com/CAMI-challenge/CAMITAX。结论当我们最初开发CAMITAX来帮助进行元基因组解释的关键评估（CAMI）计划时，它演变成一个综合软件包，可以可靠地将分类群标签分配给微生物基因组。CAMITAX可通过Apache License 2.0获得，网址为https://github.com/CAMI-challenge/CAMITAX。