ArticleMicrobiome2019
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Weight Loss and Omega-3 Supplementation Modulate the Microbiome in Women with Increased Breast Cancer Risk.Cancer prevention research (Philadelphia, Pa.) · 2026Trial
- Probiotics Augment the Effect of Non-Surgical Periodontal Treatment-A Randomised, Double-Blinded, Placebo-Controlled Trial.Journal of clinical periodontology · 2026Trial
- An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial.Frontiers in cellular and infection microbiology · 2023Trial
- Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial.Scientific reports · 2020Trial
- Farming practices exert selection pressures on the resistome of natural populations of house mice.Nature communications · 2026Article
- Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility.Nature neuroscience · 2026Article
- Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.JHEP reports : innovation in hepatology · 2026Article
- Glucuronidation metabolomic fingerprinting to map host-microbe metabolism.Nature communications · 2026Article
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- Intestinal microbiome and acute transplanted kidney rejection - results of a single-center, case-control study.BMC nephrology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Cefiderocol resistance genes identified in environmental samples using functional metagenomics.The ISME journal · 2026Article
- MaaT013 fecal microbiotherapy modulates key gastro-intestinal and immunological processes involved in GvHD pathogenesisFrontiers in microbiology · 2026Article
- Prominent mediatory role of gut microbiome in the effect of lifestyle on host metabolic phenotypes.Gut microbes · 2025Article
- Oral lipoteichoic and lipoic acids improve insulin resistance and body composition in porphyria mice on a high-carbohydrate diet.Journal of physiology and biochemistry · 2025Article
- PostbioticAnimals : an open access journal from MDPI · 2025Article
- Metagenome-guided culturomics for the targeted enrichment of gut microbes.Nature communications · 2025Article
- Roles of physical disturbance and biome properties in shaping microbial communities within Indian Ocean eddies.ISME communications · 2025Article
- Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.Microbial genomics · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundShotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data. Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline.
resultsWe present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It provides built-in support for many common operations on sequencing data and is extensible with external tools with configuration files. Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible.
conclusionsNG-meta-profiler is a high-performance solution for metagenomics processing built on NGLess. It can be used as-is to execute standard analyses or serve as the starting point for customization in a perfectly reproducible fashion. NGLess and NG-meta-profiler are open source software (under the liberal MIT license) and can be downloaded from https://ngless.embl.de or installed through bioconda.
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