title | author | date | output |
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Microbial diversity analysis using 16S rRNA gene- Trainning session with QIIME2 |
Belén Carbonetto |
March 26, 2018 |
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This session will introduce state-of-the art analysis of 16s rRNA amplicons to study microbial diversity. Participants will learn how to use QIIME2 analysis package to asses microbial community diversity and composition.
PhD students and post-doctoral researchers who are planning to use Illumina based 16S rRNA gene amplicon sequencing to study microbial diversity.
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Basic concepts of Microbial diversity analysis.
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Do quality filtering, denoising and picking of features and representative sequences with DADA2
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Assign taxonomy to features with trained classifiers.
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Align sequences and infer phylogeny.
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Calculate alpha and beta diversity.
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Test for differential abundances between groups of samples using ANCOM.
LO7.2- Decide on the subsampling depth to use for diversity calculations. How many samples are excluded?
7.3.1 - Can you observe any community structure defined by metadata categories? Is this grouping statistically significant? Can you observe the same results for all calculated distances?
7.3.2 - Which categories in metadata are most strongly associated with the differences in microbial community richness? Are these differences statistically significant? Can you observe the same results for all diveristy metrics?
8.2.1 - Which features differ in abundance across the factor selected for the analysis?