MOTIVATION: Metagenomics 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. RESULTS: Here 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.