q2-conduit

q2-conduit is a plugin that connects Conduit results to QIIME 2, acting as a converter that extracts QIIME-formatted artifacts from Conduit outputs for use in downstream analyses.

Overview¶

The Conduit software (developed by Charlie Bayne in the lab of Dr. David Gonzalez) provides a comprehensive metaproteomics workflow that combines peptide/protein identification and quantitation via DIA-NN with extensive protein annotation support, as well as data integration and GUI features designed specifically for metaproteomics.

Protein quantitation and taxonomic identification outputs from Conduit can be imported into QIIME 2, enabling seamless integration with the platform’s extensive microbiome analysis tools. q2-conduit is a QIIME 2 plugin that enables this import step.

Installation¶

q2-conduit requires a QIIME 2 installation. To install both the current QIIME 2 shotgun metagenomics (“MOSHPIT”) distribution and the q2-conduit plugin into a fresh environment named q2-conduit, run

conda env create \
 -n q2-conduit \
 -f https://raw.githubusercontent.com/biocore/q2-conduit.git/main/environment-files/q2-conduit-qiime2-moshpit-2025.7.yml

If instead installing the q2-conduit plugin into a pre-existing QIIME 2 environment, activate the QIIME 2 environment and then install the plugin repository from GitHub:

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

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

qiime dev refresh-cache

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

Usage¶

In an active QIIME environment, import the Conduit artifacts “protein_group_matrix.tsv” (the counts data) and “database_taxonomy.tsv” (the protein taxonomy information) into QIIME artifacts:

qiime tools import \
    --input-path protein_group_matrix.tsv \
    --output-path conduit_count_table.qza \
    --type ConduitCountTable

qiime tools import \
    --input-path database_taxonomy.tsv \
    --output-path conduit_taxonomy_table.qza \
    --type ConduitTaxonomyTable

With these artifacts, it is simple to extract a FeatureTable[Frequency] QIIME object containing the counts generated by Conduit, as well as a FeatureData[Taxonomy] QIIME object containing the associated proteins’ taxonomies:

qiime conduit extract \
     --i-conduit-counts conduit_count_table.qza \
     --i-conduit-taxonomy conduit_taxonomy_table.qza \
     --o-table conduit_counts.qza \
     --o-taxonomy conduit_taxonomy.qza

These objects are suitable for use in downstream QIIME functions such as qiime diversity core-metrics-phylogenetic or qiime taxa barplot, i.e., as shown below:

qiime taxa barplot \               
    --i-table conduit_counts.qza \
    --i-taxonomy conduit_taxonomy.qza \ 
    --o-visualization taxa_barplot.qzv