A TCR sequence data analysis pipeline: Tcrip

Abstract

In this chapter, we explain the T-cell receptor (TCR) sequence data analysis pipeline, Tcrip, that was developed for analyzing millions of cDNA sequence reads generated by high-throughput sequencers. Using Tcrip, we can dissect TCR-α and TCR-β sequences into specific segments and estimate the amounts and types of unique T-cell clones to characterize T-cell repertoires. Tcrip also allows us to analyze unmapped parts of the reads in detail. Then, it provides reasons for unmappability and clues to search novel exon candidate sequences. We explain the details of these algorithms.