Scripts and data resources from the HGT analysis of GMbC isolate genomes

This repository contains scripts and command lines used to generate and analyze the data presented in the manuscript "Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome."

Scripts contain command lines for:

Genome assembly, genome annotation and taxonomic calling

HGT detection and quality filtering

Annotation of transferred CDS

Core and Pan-genome analysis

Processing of shotgun metagenomics data

Data files contain:

Requests about these scripts and can be sent to Mathieu Groussin ([email protected]), Mathilde Poyet ([email protected]) or Eric Alm ([email protected]).