Installation

READ can easily be installed via PyPI and run via the command line. We also provide executables with a graphical user interface for Microsoft Windows which can be downloaded here. In-depth information on how to install and run READ can be found below.

Requirements

• Please install OpenMS.
  • [Recommended] We tested READ using OpenMS version 3.4.0!
• If you want to run READ via the command line/python, you need to either
  • install python 3.12 or 3.13,
  • or install uv (highly recommended).
• READ was tested with result files from
  • Cimerys v4.7.0 (Proteome Discoverer 3.2),
  • DIA-NN v2.2.0, and
  • Spectronaut v20.1.250624.92449
• ...but READ should also work with result files from newer software versions!
• READ supports Thermo RAW files as input on Microsoft Windows-based systems, on other operating systems please convert your RAW files to .mzML format first!
  • [Recommended] We tested READ with RAW files converted with ThermoRawFileParser version 1.4.5!
• We recommend at least 16GB of memory for running READ!

IMPORTANT

• We generally recommend using uv for running READ!
• Please also refer to Usage for more information on how to use READ with uv.

Installation

You can install READ from PyPI via pip:

pip install imp-read

Or into your uv project via:

uv add imp-read

Installation should not take longer than a few seconds!

TIP

The recommended way of using READ is via uvx which does not require installation of READ!
Please see Usage!