Course Description

This course will cover the analysis of B and T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data using bioinformatics workflows. Topics include germline allele assignment, identification of clones, and visualisation/analysis of clonal frequencies. The course will also cover emerging standards (VDJML, Change-O) in the analysis and reporting of Adaptive-immune Receptor Repertoire (AIRR) data. In addition to an introduction to software used, such as IgBLAST, pRESTO, Change-O, etc., the course will also provide an introduction to the use of Jupyter notebooks for conducting exploratory analyses and the Common Workflow Language to automate analyses.

To get a flavour of the techniques and software that will be used in the course.
IgBLAST 
pRESTO 
Change-O
Discussion site: B-T.CR

Target audience

The course was designed for experimentalist and students who want to explore adaptive immune repertoires using NGS data.
Individuals that are working - or looking forward to work - in the area of T cell or B cell receptor analysis will benefit from attending this training course.

Pre-requisites

Basic knowledge of the process of T and B cell receptor generation is essential.
Knowledge and data handling of file formats used in next generation sequencing analysis (FASTQ, SAM/BAM) highly desirable.
Familiarity with use of the Unix/Linux command line.
Basic knowledge of Python desirable, but not essential.