Estimate Alpha and Beta Diversities
The Estimate Alpha and Beta Diversities template workflow takes an abundance table with sequences as input. If your data is amplicon sequencing data use this workflow. Otherwise use Merge and Estimate Alpha and Beta Diversities (Merge and Estimate Alpha and Beta Diversities).
Remember to add metadata to the abundance table before starting the workflow. Adding metadata can be done very early on, by importing metadata and associating reads to it before generating an abundance table. The metadata will propagate to the abundance table automatically. When working with reads that were not associated with metadata in the first place, it is always possible to add metadata to an already existing abundance table with the tool Add Metadata to Abundance Table (Add Metadata to Abundance Table).
The workflow is available at:
Workflows | Template Workflows () | Microbial Workflows (
) | Metagenomics (
) | Amplicon-Based Analysis (
) | Estimate Alpha and Beta Diversities (
)
The first tool of the workflow is Refine Abundance Table which filters features with less than 10 combined abundance. The output is a reduced abundance table that will be used as input for downstream analysis:
- Align OTUs with MUSCLE, a tool that will produce an alignment used to reconstruct a Maximum Likelihood Phylogeny (see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Maximum_Likelihood_Phylogeny.html), which will in turn output a phylogenetic tree also used as input in the following two tools.
- Alpha diversity.
- Beta diversity.
Running this workflow will therefore give the following outputs: a phylogenetic tree of the sequences, a diversity plot for the alpha diversity and a PCoA plot for the beta diversity.