miRCat2 preconfigured Workflow

miRCat2 is a miRNA prediction pipeline, suitable for both animal and plant data.

This workflow consists of two stages including the datasetup stage.

  1. Database setup
  2. miRCat2 setup

A set of tutorial data for miRCat2 can be found here.

Further information on the export options available to miRCat can be found here.

As of version 4.5 of the Small RNA Workbench, we have included a much faster version of miRCat2 known as the ‘standalone’ version. This was developed as some users experienced long waits to obtain results due to the low memory database feature. Therefore, if you have the memory (RAM) available and you are running miRCat2 from the command-line, we recommend using the standalone version.

miRCat2 standalone version does exactly the same as the standard miRCat2 workflow, i.e. same input, output, and algorithm. The only difference in this version is that it does not use the Workbench database, it relies on the personal machine memory. It only works through the command-line, and to use it add the flag “-standalone” to the command-line parameters.

You can run miRCat2 standalone through the command-line using the following command:

java -jar Workbench.jar -tool mircat2 -config configFile.json [-standalone]



A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices