ArticleGigaScience2020
CAMITAX: Taxon labels for microbial genomes.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genomic characterization of an extensively drug-resistant Klebsiella pneumoniae co-harboring mcr-3.11, blaNDM-5 and blaCTX-M-27 isolated from pelvic effusion in a colon cancer patient.BMC microbiology · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.Briefings in bioinformatics · 2024Article
- MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies.Nature communications · 2024Article
- In Vitro Interaction betweenMicroorganisms · 2024Article
- Critical Assessment of Metagenome Interpretation: the second round of challenges.Nature methods · 2022Article
- Multi-Omics Characterization of Host-DerivedFrontiers in microbiology · 2021Article
- Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies.Frontiers in genetics · 2021Article
- CAMITAX: Taxon labels for microbial genomes.GigaScience · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
findingsWe 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.
conclusionsWhile 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.
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