Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
MetadataShow full item record
AbstractBACKGROUND: 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.
CitationGigascience. 2020 Jan 1;9(1). pii: 5698015. doi: 10.1093/gigascience/giz154.
AffiliationBRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.
The following license files are associated with this item:
- Creative Commons
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-ShareAlike 4.0 International
- Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.
- Authors: Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA
- Issue date: 2017 Nov 28
- Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.
- Authors: Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC
- Issue date: 2019 Jun 4
- GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.
- Authors: Boyd JA, Woodcroft BJ, Tyson GW
- Issue date: 2018 Jun 1
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
- Authors: Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N
- Issue date: 2020 May 19
- Gene content dissimilarity for subclassification of highly similar microbial strains.
- Authors: Tu Q, Lin L
- Issue date: 2016 Aug 17