Bile acid diarrhoea PhD project
I have around 200 samples. Metagenomic shotgun- sequenced at a depth of 50 million reads per sample.
I would like to use
- BBDuk (Decontamination Using Kmers) to trim adapters and other quality controls
- MetaPhlAn3 (Metagenomic Phylogenetic Analysis) to a profile the composition of microbial communities from
- HUMAnN3 (HMP Unified Metabolic Analysis Network) to profile the abundance of microbial metabolic pathways and other molecular functions. I will also use FastQC and MultiQC before and after QC to check quality of reads.
The aim of this study is to compare the bacterial profile and functional gene profile between bile acid diarrhoea (BAD) patients, irritable bowel syndrome (IBS) patients and healthy controls .