ArticleMicrobiome2017
MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.
Article in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Lactobacillus-vectored nanobodies improve broiler productivity under sub-clinical necrotic enteritis with associated microbiome and transcriptome changes.NPJ biofilms and microbiomes · 2026Article
- 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
- Soil microbial adaptation to carbon deprivation: shifts in lignocellulolytic gene profiles following long-term plant exclusion.Environmental microbiome · 2025Article
- MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data.Genes & genomics · 2024Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- SnakeLines: integrated set of computational pipelines for sequencing reads.Journal of integrative bioinformatics · 2023Article
- Article
- PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.Life (Basel, Switzerland) · 2022Article
- Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge.BMC genomics · 2022Article
- ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing.Bioinformatics (Oxford, England) · 2022Article
- Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome.Communications biology · 2022Article
- Article
- Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories.Veterinary sciences · 2021Article
- Impact of concurrency on the performance of a whole exome sequencing pipeline.BMC bioinformatics · 2021Article
- NGS read classification using AI.PloS one · 2021Article
- gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.NAR genomics and bioinformatics · 2020Article
- TAMA: improved metagenomic sequence classification through meta-analysis.BMC bioinformatics · 2020Article
- Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics.Scientific reports · 2020Article
- Article
- SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.Genome biology · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools.
resultsWe propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases.
conclusionsIn a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.