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Microbiome_​Analysis

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 corresponding 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

Gut Microbiome Analysis of Inflammatory bowel disease (IBD) Patients (16S)This workflow downloads environmantal DNA in the form of 16S amplicon sequences from ENA and anayzes it to create and comparetaxonomic profiles of a microbial community. DADA2 R package required General overview of gut microbial compositionhealthy vs sickA series of R nodes matching DADA2 pipeline steps to generate ASV table. Generate taxonomic profiles from amplicon sequence variant (ASV) tables.Taxonomic rank can be selected.Visualise taxonomic profilesacross patients and timepointsDownload FASTQfiles from ENA MicrobialComposition Run DADA2 Routine Generate TaxonomicProfiles Prepare EssentialVariables Compare TaxonomicProfiles Gut Microbiome Analysis of Inflammatory bowel disease (IBD) Patients (16S)This workflow downloads environmantal DNA in the form of 16S amplicon sequences from ENA and anayzes it to create and comparetaxonomic profiles of a microbial community. DADA2 R package required General overview of gut microbial compositionhealthy vs sickA series of R nodes matching DADA2 pipeline steps to generate ASV table. Generate taxonomic profiles from amplicon sequence variant (ASV) tables.Taxonomic rank can be selected.Visualise taxonomic profilesacross patients and timepointsDownload FASTQfiles from ENA MicrobialComposition Run DADA2 Routine Generate TaxonomicProfiles Prepare EssentialVariables Compare TaxonomicProfiles

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: dadi
Created at: 2020-06-05
On NodePit since: 2020-06-11
Last update: 2024-11-18
Created with KNIME version: v4.4.1
Tags: life sciencesbioinformaticsmetagenomicssequence analysismicrobiomeamplicon sequence16S rRNA

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