Following the data preparation, this video attempt to outline some simple analysis in microbiome analysis and how it can be done simply with a wide varieties of tools.
Email: [email protected]
Website: https://www.liquidbrain.org/videos
Patreon: https://www.patreon.com/liquidbrain
Github: https://github.com/brandonyph/LiquidBrain_Scripts
MiSeq SOP: https://mothur.org/wiki/miseq_sop/
MEGAN6: https://computomics.com/services/megan6.html
Galaxy: https://usegalaxy.org/
Chapters:
0:00 Introduction
0:33 Inputs required
1:13 Analyses Included in this video
2:21 Goals for this video
4:23 Looking at the input files format
7:57 OTU identification and clustering
12:00 Phylotype Analysis
13:59 Alpha and Beta Diversity
19:25 PCA output in R
21:47 AMOVA between treatments
25:47 ggtree for tree plotting in R
29:10 Customization of ggtree
33:10 Galaxy + Krona
36:50 MEGAN6
41:35 Closing summary