ArticleBMC genomics2019
Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes.Environmental microbiome · 2025Article
- Soil microbial responses to multiple global change factors as assessed by metagenomics.Nature communications · 2025Article
- Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.mBio · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.Journal of assisted reproduction and genetics · 2025Review
- Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.ISME communications · 2025Article
- Exploring protein natural diversity in environmental microbiomes with DeepMetagenome.Cell reports methods · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.Microbiome · 2024Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- Rodents consuming the same toxic diet harbor a unique functional core microbiome.Animal microbiome · 2024Article
- Article
- Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.Nature communications · 2024Article
- An in-depth evaluation of metagenomic classifiers for soil microbiomes.Environmental microbiome · 2024Article
- Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan.Microorganisms · 2024Article
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3 authors.
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Abstract
backgroundMetagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.
resultsWe have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled).
conclusionsAlthough differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.
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