biomodal duet multiomics software documentation

Welcome to the biomodal duet multiomics solution bioinformatics documentation hub. In this space, you will find everything you need to install, run, and interpret data generated with the duet evoC and duet +modC multiomics solutions.

Software Overview

The biomodal duet multiomics software provides a comprehensive solution for analyzing biomodal data. It includes tools for data processing, analysis, and visualization, making it easier for researchers to gain insights from their data.

The overall structure of the software is in two parts:

1. The duet pipeline and the biomodal CLI tool to download and use it.

2. The modality XPLR software, which takes the output from the duet pipeline and allows the user to generate detailed statistics and visualisations.

This diagram shows the overall workflow to for using biomodal software:

The duet pipeline

The structure of the biomodal duet pipeline and biomodal CLI is shown in this diagram:

The typical user flow for the duet pipeline is as follows:

1. Download and install the biomodal CLI.

2. Define your instance location by setting the BIOMODAL_INSTANCE_DIRECTORY environment variable.

3. Run biomodal init to set up the necessary configuration files.

   • This will automatically download the latest version of the duet pipeline software.

4. Run biomodal run duet --test to make sure your system is properly configured.

   • Includes downloading a small test dataset and running the duet pipeline on it.

5. Run biomodal run duet with the proper settings to run the pipeline on your data.

   • Based on this example.

6. Read and interpret the results.

   • Further guidance on interpreting the outputs from the pipeline can be found in the data interpretation guide.

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Other Capabilities

• You can download new versions of the duet pipeline software by running biomodal download.

• You can maintain multiple versions of the duet pipeline software on your system and choose to analyse with whichever you choose.

• The biomodal CLI also allows you perform other tasks, including:

  • Gathering relevant support information about your system with biomodal get diagnostics.

  • Generating support for a new reference genome with the reference genome pipeline.

modality XPLR

The duet pipeline performs the core processing steps to generate alignments, variant calls, and methylation calls.

To continue the analysis and look for biological insight from the data, biomodal has created modality XPLR, a command line analysis tool that extracts methylation data, generates statistics, and produces visualisations and reports. More details of modality XPLR and it capabilities can be found in the modality XPLR documentation.

Available guides

duet software installation and running guide

Learn in detail how to download, install and run the command line interface (CLI) for processing data.

data interpretation guide

To understand the outputs of the duet pipeline, refer to the data interpretation guide for duet +modC and duet evoC

modality XPLR

Once you have outputs from the duet pipeline, learn how to explore your methylation data in more depth with the modality XPLR software, as described in this guide.

📝 Learn about the analysis workflow.	📁 Learn about the output files.	📈 Learn about the analysis metrics and summary report.

Other available resources

1. Release notes

2. Demo data sets

3. Duet software license

4. Earlier CLI release 1.1.3 with duet 1.4.2 documentation