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Autism FMT analysis notes

This repository contains 16S and virome analysis software and data for our original paper and our eighteen follow-up paper.

Original paper

Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms. Kang, D, Adams, JB, Gregory, A, Borody, T, Chittick, L, Fasano, A, Khoruts, A, Geis, E, Maldonado, J, McDonough-Means, S, Pollard, EL, Roux, S, Sadowsky, MJ, Lipson, KS, Sullivan, MB, Caporaso, JG, and Krajmalnik-Brown, R. Microbiome (2017). DOI: 10.1186/s40168-016-0225-7.

Corresponding sample metadata is here.

Microbiome analysis notebooks and software

Software and Jupyter notebooks for the microbiome analyses were primarily developed by J Gregory Caporaso (Caporaso Lab, Center for Microbial Genetics and Genomics, Northern Arizona University). These can be found in the 16S directory of this repository. Questions should be directed to gregcaporaso@gmail.com.

Microbiome analysis commands are here.

Virome analysis software and data

Data and software supporting the virome analyses were primarily developed by Ann Gregory (Sullivan Lab, Ohio State University). These can be found the virome directory of this repository. Questions should be directed to anin.gregory@gmail.com.

Eighteen-month follow-up (currently in review)

Corresponding sample metadata is here.

The analysis code has been updated to use QIIME 2, and can be found in the 18-month-followup branch of this repository.

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