Environment setup

To use SCRuB’s QIIME2 plugin, you must have run both the SCRuB R and QIIME2 installation commands shown here from within a QIIME2 environment. The summary of the plugin’s inputs and outputs are as follows:

Inputs

  1. table
    • The table is of the Qiime2 type FeatureTable[Frequency], where the rows are features (e.g. ASVs/microbes), the columns are samples, and the entries are the number of sequences for each sample-feature pair. This table must be of shape n_taxax( n_samples + n_controls ), where n_samples is the number of samples, n_controls is the number of negative controls, and n_taxa is the number of features in the count matrix
  2. metadata
    • This is a QIIME2 formatted metadata (e.g. tsv format) where the rows are samples matched to the (1) table and the columns are different sample data (e.g. time point).
  3. ( Optional ) control_idx_column
    • This is the name of the column in the (2) metadata that indicates the which samples should be treated as negative controls. If not specified, will identify negative controls by searching for a metadata column of ‘empo_2’ or ‘qiita_empo_2’, and identifying which entries contain the keyword ‘negative’
  4. ( Optional ) sample_type_column
    • This is the name of the column in the (2) metadata that indicates the sample type, which specifies the groupings of negative controls SCRuB should use for decontamination. Default is ‘sample_type’
  5. ( Optional ) well_location_column
    • This is the name of the column in the (2) metadata that indicates the well of each sample, which specifies the groupings of negative controls SCRuB should use for decontamination. Default is ‘well_id’
  6. ( Optional ) control_order
    • specifies the ordering which the negative controls from sample_type should be run. Default input (NA) uses the ordering in which the sample are found in the metadata table.
  7. output-dir
    • The desired location of the output file

Outputs

Depending on the interface, SCRuB’s Qiime2 pliugin either:
1) Writes the decontaminated .qza format table to the specified path (Qiime2 and Command line interface)
2) returns a dataframe of decontaminated samples (Python interface)

For more detail, please refer to the QIIME2 Tutorial, or refer to the jupyter notebooks found here.