The Downstream Analysis pipeline provides sample observation and taxonomic summaries and diversity analyses of an OTU table using QIIME 2.
BIOM File: The biom file contains the OTU and taxonomy tables to be analyzed. This pipeline accepts BIOM V1 or QIIME's BIOM V2 format. All biom files produced by Nephele's amplicon pipelines should work.
Mapping File: The mapping file contains the metadata about the samples which will be used in the analysis. The mapping file format is the same as that used by the amplicon pipelines (SE or PE templates). The FASTQ file columns will be ignored. Only samples listed in the mapping file will be included in the pipeline results. So, if you want to analyze only a subset of the samples in your biom file, you can submit the mapping file with only those samples, and the others will be excluded from the analysis.
Tree File (Optional): The tree file contains a rooted phylogenetic tree with tip labels that correspond to the OTU names in the BIOM file. The pipeline accepts Newick format (.nwk). OTUs that are in the BIOM file and not in the tree will be filtered from the BIOM file before analysis. The tree file is optional; see "diversity core-metrics-phylogenetic" in Pipeline Steps for additional analyses that will be run if it is uploaded.
Sampling depth: The total frequency that each sample should be rarefied to prior to computing diversity metrics. Samples with counts below this value will be removed from the analysis. If you are using the output of a Nephele amplicon pipeline, you may find it useful to consult otu_summary_table.txt which lists the sample counts.
Alpha group significance: Run alpha diversity statistical comparisons between groups, and produce alpha diversity plots. This step runs after samples with counts below your sampling depth are filtered from your biom and mapping files. It requires the filtered mapping file's Treatment Group column to contain at least 2 groups, and each group to contain at least 2 samples.
If you are not sure which samples and groups will remain after the sampling depth filtering, run the job first with this option unchecked, and review the summary.qzv file. If you are using the output of a Nephele amplicon pipeline, you may find it useful to consult otu_summary_table.txt which lists the sample counts.
.qzv files can be viewed on QIIME 2's view page. See QIIME 2's information about the output formats and for help with the view page. Where possible, the
.qza artifacts are also exported to their native format in directories of the same name. The following plugin methods are used: