Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding

This repository includes all the source code, tests and notebooks to generate the figures used in the (Song et al. 2021). Each analysis step is outlined here.

Notes to the reader

While we do not provide all the data in this repository we provide the BIOM tables, sample information, alpha and beta diversity tables. The raw and quality controlled sequences from which the BIOM table originates can be found in Qiita study 10894, 10249, and 1718 (remember to login).

Sequence data have been deposited at European Bioinformatics Institute (EBI) under study accession number ENA: ERP120105, ENA: ERP016173 and ENA: ERP120109.

Repository Structure

• code

This directory contains the code (as notebooks) for each step in a numerically organized format. More descriptions can be found within the README file for that directory.

• data

This directory contains the input data, along with some output from computationally expensive tools.