Aim:
Process metagenomics data using metadata groups ( --metadata metadata.tsv )to enable the generation of alpha and beta diversity analyses
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Running nfcore/ampliseq with metadata information
Metadata is optional to run the ampliseq pipeline, but for performing downstream analysis such as barplots, diversity indices (alpha and beta diversities) or differential abundance testing, a metadata file is essential.
The public data we are using in the workshop does not have associated metadata information, so we will used an ‘artificially’ created metadata.tsv file that assigns the first 15 samples to a “control” group and the remaining samples to a group called “illumina” (technology used to created the amplicon data.
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Print the content of the metadata file (e.g., cat metadata.tsv):
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ID condition Illumina1 control Illumina2 control Illumina3 control Illumina4 control Illumina5 control Illumina6 control Illumina7 control Illumina8 control Illumina9 control Illumina10 control Illumina11 control Illumina12 control Illumina13 control Illumina14 control Illumina15 control Illumina16 illumina Illumina17 illumina Illumina18 illumina Illumina19 illumina Illumina20 illumina Illumina21 illumina Illumina22 illumina Illumina23 illumina Illumina24 illumina Illumina25 illumina Illumina26 illumina Illumina27 illumina Illumina28 illumina Illumina29 illumina Illumina30 illumina Illumina31 illumina Illumina32 illumina Illumina33 illumina Illumina34 illumina Illumina35 illumina Illumina36 illumina Illumina37 illumina Illumina38 illumina Illumina39 illumina Illumina40 illumina Illumina41 illumina Illumina42 illumina Illumina43 illumina Illumina44 illumina Illumina45 illumina Illumina46 illumina Illumina47 illumina Illumina48 illumina Illumina49 illumina Illumina50 illumina Illumina51 illumina Illumina52 illumina Illumina53 illumina Illumina54 illumina Illumina55 illumina Illumina56 illumina Illumina57 illumina Illumina58 illumina Illumina59 illumina |
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Move to the /results/qiime2/diversity folder and evaluate the alpha diversity results, particularly, open the interactive “index.html” reports for each type of alpha diversity generated:
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Move to the /results/qiime2/diversity folder and evaluate the beta diversity results, particularly, open the interactive “index.html” reports for each type of beta diversity generated:
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