SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine.

Motivation: Profiling the T cell receptor (TCR) repertoire using next-generation sequencing (NGS) to quantify adaptive immune responses has become common in human and animal research. Companion dogs with spontaneous tumors have similarities with humans who have cancer. T cells undergo clonal expansion when they recognize specific antigens via surface TCRs. TCR counts from NGS data provide a way to quantify T cell response to vaccines, cancer, or infectious diseases for preclinical and clinical health studies. One complication is that the power and accuracy of TCR experiments depend substantially on the TCR sequencing depth, therefore it is important to determine the optimal read depth of an experiment to verify whether a subject's repertoire is correctly represented. Results: The optimal TCR sequencing depth for future experiments can be determined by randomly sampling lower TCR sequencing depths from a sequencing experiment, assembling the TCR clonotypes, and determining where the saturation of power and accuracy occurs. Moreover, one can determine whether an existing experiment has sufficient sequencing depth to justify its conclusions. We provide guidelines to determine whether the sequencing depth is adequate and a computational pipeline that:Samples pairs of sequences and assembles clonotypesSummarizes the results in a parametrized report.