ArticleScientific data2024
Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.
Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Standardized 16S Meta-Analysis Reveals Consistent Host-Associated Patterns in Laminariales Epiphytic Microbiomes.MicrobiologyOpen · 2026Pooled it
- Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.mSystems · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Fungal ecology in the age of 'omics.The New phytologist · 2026Review
- Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.PLoS computational biology · 2026Article
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
- Review
- Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.BMC oral health · 2025Article
- Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.mSystems · 2025Article
- Gut microbiota in irritable bowel syndrome: a narrative review of mechanisms and microbiome-based therapies.Frontiers in immunology · 2025Review
- Metagenomic analysis of the camel rumen archaeome and its functional potential.Frontiers in veterinary science · 2025Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.Scientific data · 2024Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.
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