Gut Microbiome Analysis of IBD Patients (16S)

This workflow investigates the composition of gut microbial communities from individuals with inflammatory bowl disease (IBD). Samples were taken from 10 donors (1x) and 10 patients (3x) before and after a gut microbiome transplant at different time points. The V1 and V2 region of the 16S ribosomal RNA gene sequence were sequenced from total of 40 samples using 454 GS FLX Titanium sequencer. The coresponding sequences, with accession ID PRJDB4959 will be downloaded from ENA. The workflow uses the DADA2 R package by Callahan et al. to determine the microbial composition from the 16S sequences. The DADA2 R package needs to be installed for the workflow to work. Installation instructions can be found at https://benjjneb.github.io/dada2/dada-installation.html MANUAL: DADA2 Software instalation manual https://benjjneb.github.io/dada2/dada-installation.html


This is a companion discussion topic for the original entry at https://kni.me/w/XCb9Cfe1a2wDc78I