ImReP tutorial

ImReP tutorial

ImReP is a tool written in Python programming language (version 2.7) which is designed to assemble CDR3 region sequences from RNA- or TCR-(BCR-)-Seq reads (either single- or paired-end) and provide immune repertoire as a set of clonotypes with their counts.

We assume you have a basic knowledge of sequence analysis and of Unix-based operating systems (although you should be able to run the pipeline on MacOS, some commands may require modification). If you have limited knowledge of UNIX, we encourage you to follow the Unix Tutorial.

In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output.

• What is ImReP?
• Installation instructions
• Running ImReP
• ImReP input
• Examples
• ImReP output

Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.