This repository contains command lines used to generate the data presented in the manuscript "A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research."

Command lines are grouped by categories:

1. Analysis of all sanger 16S sequences generated from the BIO-ML isolates
2. Genome assembly, genome annotation and taxonomic calling
3. SNP calling
4. Core and Pan-genome analysis
5. Processing of NGS (16S and metagenomics) data

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