<p>This project encompasses a suite of scripts that I have developed in the course of my PhD to analyse T-cell receptor (TCR) repertoire data produced by deep-sequencing. Functions include fastq preparation, TCR analysis (built on Decombinator), error-correction and CDR3 translation and extraction.</p>
<p>It also provides an alternative set of V and J gene tags for alpha/beta TCRs. This extended tag set permits detection of rearrangements that make use of all prototypic TCR alleles, regardless of IMGT-defined functionality (i.e. it includes ORF and P as well as F genes), some of which can be shown to regularly partake in recombination.</p>
<p>These scripts have been developed whilst under the supervision of Prof. Benjamin Chain, and often build on code produced by my colleagues Dr. Niclas Thomas or Katharine Best (where indicated in comments).</p
