q2-exonerate

q2-exonerate is a QIIME 2 plugin for the Exonerate toolkit.

Installation

You can install q2-exonerate using mamba in an existing QIIME 2 environment by following the steps described below.

• Make sure to start by installing mamba in your base environment:

  conda install mamba -n base -c conda-forge

• Activate your QIIME 2 environment (ver 2022.8 or later, see the official user documentation) and install relevant dependencies:

  conda activate qiime2-{ENV_VERSION}
  mamba install -c bioconda -c conda-forge exonerate

• Install q2-exonerate:

  pip install git+https://github.com/bokulich-lab/q2-exonerate.git

• To see that everything worked, refresh cache and check QIIME2 help:

  qiime dev refresh-cache
  qiime exonerate --help

Usage

Currently, only one action is available in the plugin - simulate-pcr - it can be used to carry out an in-silico PCR using a set of template sequences and primers of choice.

1. First, import the list of PCR experiments to run - please check the Ipcress documentation for information about the file format:

   qiime tools import \
     --type IPCRessExperiments \
     --input-path <path-to-experiment-file> \
     --output-path ipcress_exp.qza

2. Then, to simulate a PCR experiment, run the following command:

   qiime exonerate simulate-pcr \
     --i-experiments ipcress_exp.qza \
     --i-templates <path-to-templates> \
     --o-products pcr_products.qza  \
     --o-product-metadata pcr_metadata.qza \
     --verbose

   where:

   • --i-experiments is a path the the qza file generated in step 1)
   • --i-templates is a path to a FeatureData[Sequence] artifact containing desired PCR templates
   • --o-products is a path to a FeatureData[Sequence] artifact which will contain all the identified PCR product sequences
   • --o-product-metadata is a path to a PCRProductMetadata artifact which will contain additional information about all the identified PCR products.

3. Optionally, you can tabulate the list of PCR product metadata and display it as a QIIME2 visualization:

   qiime metadata tabulate \
     --m-input-file pcr_metadata.qza \
     --o-visualization pcr_metadata.qzv

License

q2-exonerate is released under a BSD-3-Clause license. See LICENSE for more details.