IgG-Seq in PI-ME/CFS Repository

Primary Code Author: Kathryn E McCauley

Date of Release: TBD

Version: 1.0

License Details: Public Domain

This is the code for figures and tables associated with a manuscript in preparation titled:

"Functional Enrichment of Immune Targeted Gut Microbiota in Post-Infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome"

Kathryn E. McCauley¹, Carlotta Vizioli², Ayaan Ahmed³, Shreni Mistry⁴, Andrew S Burns⁴, Darrell E Hurt¹ OR Mariam Quiñones¹, Avindra Nath², Brian Walitt ², Jennifer J. Barb³

¹Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
²National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
³Translational and Biobehavioral Health Promotion Branch, National Institutes of Health, Clinical Center, Bethesda, MD, USA
⁴NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA

Sequence and Analysis Data

Raw Sequence Reads

Raw sequence reads are available from the Sequence Read Archive at: PRJNA954397.

Reads were processed with Nephele's DADA2 pipeline with the parameters described in the manuscript. After completion of the pipeline, the results archive was downloaded and key components can be found in the data/proc directory.

This repository includes all code and data needed to reproduce figures in the manuscript.

PICRUSt2 Code

Code to generate PICRUSt2 data was as follows:

picrust2_pipeline.py -s data/proc/Autol_process_pool/seq.fasta \
    -i data/proc/Autol_process_pool/taxa.biom \
    -o data/proc/full_picrust2

Only files used in analysis are stored in this repository.