Installation

System Requirements

  • IMDA is available for Windows and Linux operating systems (64-bit)
  • Installed memory (RAM): minimum 16 GB
  • Python 3.7
  • Java
  • Perl (for Bowtie2)

Download

Please download the newest version here: ImmunoDataAnalyzer

Additional data for testing IMDA can be downloaded here: test data set

An examplary library for Undetermined Read Analysis created with bowtie2-build command including TCR and PHIX reads can be downloaded here: TCRPHIX library

Third party software

IMDA uses third party software that is developed independently and need to be downloaded and installed for certain features to work.

MIGEC

MIGEC is a commandline tool for preprocessing sequencing data including de-multiplexing and UMI tag extraction for multiple FASTQ files. Learn more about MIGEC.

If preprocessing with MIGEC is needed, download MIGEC version 1.2.9 here.

Warning

IMDA has been implemented and tested using MIGEC version 1.2.9. Please make sure you download MIGEC version 1.2.9, otherwise IMDA’s MIGEC analysis feature might not work properly.

MiXCR

MiXCR is a commandline tool for fast and accurate analysis of T and B cell receptor repertoire sequencing data. Learn more about MiXCR.

Download MiXCR in version 3.0.13 here.

Warning

IMDA has been implemented and tested using MiXCR version 3.0.13. Please make sure you download MiXCR version 3.0.13, otherwise IMDA’s MiXCR analysis feature might not work properly.

VDJtools

VDJtools is a framework for analysis of immune repertoire sequencing data. We use VDJtools for the calculation of various diversity indices. Learn more about VDJtools.

Download VDJtools in version 1.2.1 here.

Warning

IMDA has been implemented and tested using VDJtools version 1.2.1. Please make sure you download VDJtools version 1.2.1, otherwise IMDA’s VDJtools analysis feature might not work properly.

Bowtie2

Bowtie2 is a tool for aligning sequencing reads to short and long reference genes. We use Bowtie2 for undetermined read analysis. Learn more about Bowtie2.

Download Bowtie2 in version 2.3.4 here.

Warning

IMDA has been implemented and tested using Bowtie2 version 2.3.4. Please make sure you download Bowtie2 version 2.3.5.1, otherwise IMDA’s Bowtie2 analysis feature might not work properly.

Java

The third party tools need the Java Runtime Environment to be installed on your machine.

Please download the Java Runtime Environment 64bit here.

Perl

The third party tools need Pearl to be installed on your machine.

Please download Perl here.

Setup

  • Carefully read the License agreement and proceed only if you agree to the terms and conditions.