TRAPeS (TCR Reconstruction Algorithm for Paired-End Single-cell): a Python/ C++ package for efficiently extracting T cell receptor sequences from standard, short-read single cell RNA-seq libraries. Download it here.
Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state/ Shaked Afik, Kathleen B Yates, Kevin Bi, Samuel Darko, Jernej Godec, Ulrike Gerdemann, Leo Swadling, Daniel C Douek, Paul Klenerman, Eleanor J Barnes, Arlene H Sharpe, W. Nicholas Haining, Nir Yosef. BiorXiv (2017). doi: https://doi.org/10.1101/072744