q2-surpi

q2-surpi is a plugin that connects SURPI+ results to QIIME 2 for analysis. The below workflow shows that q2-surpi acts as a converter, extracting QIIME-formatted artifacts from SURPI+ outputs for use in downstream analyses.

Installation

q2-surpi requires an existing QIIME 2 environment (see documentation at https://docs.qiime2.org for QIIME 2 installation instructions). To install the plugin, first activate the QIIME 2 environment and then install the plugin repository from github:

pip install git+https://github.com/biocore/q2-surpi.git

After this, it is necessary to refresh the QIIME 2 plugin cache:

qiime dev refresh-cache

The q2-surpi plugin should now be in the list of installed plugins produced by running qiime --help

Usage

In an active QIIME environment, import the SURPI+ count table of interest and the SURPI-compatible sample sheet into QIIME artifacts:

qiime tools import \
    --input-path surpi_output.counttable \
    --output-path surpi_output.qza \
    --type SurpiCountTable

qiime tools import \
    --input-path surpi_sample_info.csv \
    --output-path surpi_sample_info.qza \
    --type SurpiSampleSheet

With these artifacts, it is simple to extract a FeatureTable[Frequency] QIIME object containing the counts generated by SURPI, as well as a FeatureData[Taxonomy] QIIME object containing the associated taxonomies.
Assuming that the SURPI sample sheet is linked to the counttable files by barcode IDs, this can be accomplished by running:

qiime surpi extract \
     --i-surpi-output surpi_output.qza \
     --i-surpi-sample-info surpi_sample_info.qza \
     --o-table surpi_counts.qza \
     --o-taxonomy surpi_taxonomy.qza

Alternatively, if the sample sheet and counttable files are linked by the Sample_ID values, the command can be altered to set the optional --p-ids-are-barcodes parameter to False

qiime surpi extract \
     --i-surpi-output surpi_output_by_sample_id.qza \
     --i-surpi-sample-info surpi_sample_info.qza \
     --p-ids-are-barcodes False \
     --o-table surpi_counts.qza \
     --o-taxonomy surpi_taxonomy.qza

These objects are suitable for use in downstream QIIME functions such as qiime diversity core-metrics-phylogenetic or qiime taxa barplot.