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 (mgroussi@mit.edu), Mathilde Poyet (mpoyet@mit.edu) or Eric Alm (ejalm@mit.edu).