Genome-centric metagenomics — the study of communities using shotgun-sequencing to recover microbial genomes — has become the primary method for us to discover species and their fundamental roles in ecosystems everywhere. In this talk I will present several new bioinformatic methods, many of which were developed by Rhys Newell, a recently submitted PhD student. They improve upon the state of the art in two critical steps in this process: short+long read hybrid assembly, and clustering assembled contigs into sets representing draft genomes (“binning”). Rhys also developed Lorikeet, a variant calling algorithm which has significantly better accuracy and runtime than current tools. I will present these results and their application to understanding the evolution of strains using global-scale metagenomic data. Each of the methods is freely available including a comprehensive pipeline for recovering genomes from raw reads, at https://research.qut.edu.au/cmr/software and https://sandpiper.qut.edu.au.