ArticleBioinformatics (Oxford, England)2024
ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- K-MARVEL: K-Mer-based antimicrobial resistance virtual exploration lab.Nature communications · 2026Article
- The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.FEMS microbiology ecology · 2026Review
- Article
- Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.Microbiology spectrum · 2026Article
- Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.Antibiotics (Basel, Switzerland) · 2026Article
- Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.Microbiology spectrum · 2026Article
- Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.Frontiers in microbiology · 2026Article
- Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.Nature communications · 2025Article
- Characterization of antibiotic determinants and heavy metal resistance genes inMicrobial genomics · 2025Article
- Data-Driven Approaches in Antimicrobial Resistance: Machine Learning Solutions.Antibiotics (Basel, Switzerland) · 2024Article
- High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationAnalyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind.
resultsIn this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs. ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14 078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. ARGextender is a bioinformatic approach combining KMA and SPAdes to recruit reads for a targeted de novo assembly. While our aim is on ARGs, the pipeline also creates Mash sketches for fast searching and comparisons of sequencing runs. AVAILABILITY AND IMPLEMENTATION: The ARGprofiler pipeline is a Snakemake workflow that supports the reuse of metagenomic sequencing data and is easily installable and maintained at https://github.com/genomicepidemiology/ARGprofiler.
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Registered trials
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.