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

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.