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 Dr. Charles 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. Protein quantitation and taxonomic identification outputs from Conduit can be imported into the QIIME 2 software to enable instant integration with that platform’s extensive analysis features. 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