Shotgun Qiita Plugin

Qiita (canonically pronounced cheetah) is an analysis environment for microbiome (and other "comparative -omics") datasets.

This package includes the Shotgun functionality for Qiita. Currently, we have:

• HUMAnN2

Note that is suggested that you download the full databases once this package is installed by:

$ humann2_databases --download chocophlan full $DIR
$ humann2_databases --download uniref diamond $DIR

The default pipeline is:

1. Run HUMAnN2 on per sample FASTQ
2. Collate individual results into single OTU tables: gene families, path coverage and path abundance.
3. Renormalize the tables: gene families - CPM, path coverage - relative abundance, path abundance - relative abundance.
4. Stratify the renormalized tables.

Note that HUMAnN2 depends on metaphlan2 but neither the HUMAnN2 or this plugin automatically install that dependency. Remember that you need to put the db_v20 folder in the path that the metaphlan2.py executable.