ArticleBioinformatics (Oxford, England)2019
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.BMC microbiology · 2026Article
- Tumor microbiome differences in early-onset versus average-onset pancreatic adenocarcinoma.ESMO gastrointestinal oncology · 2025Article
- Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.Applied and environmental microbiology · 2024Article
- Current Trends and Challenges of Microbiome Research in Prostate Cancer.Current oncology reports · 2024Review
- The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.Nutrients · 2022Review
- Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.Microbiome · 2022Article
- Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs.NPJ biofilms and microbiomes · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.Nucleic acids research · 2021Article
- Metagenomic analysis of the cow, sheep, reindeer and red deer rumen.Scientific reports · 2021Article
- Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos.BMC microbiology · 2020Article
- 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding.Genome biology · 2020Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
- Article
- Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes.Molecular biology and evolution · 2020Article
- New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era.Frontiers in microbiology · 2020Review
- CAMITAX: Taxon labels for microbial genomes.GigaScience · 2020Article
- Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.Genome biology · 2019Article
- Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery.Nature biotechnology · 2019Article
- Characterisation of the British honey bee metagenome.Nature communications · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationMetagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near-complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterize thousands of genomes simultaneously, to enable identification and functional characterization.
resultsHere we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree. AVAILABILITY AND IMPLEMENTATION: MAGpy is available on github: https://github.com/WatsonLab/MAGpy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.