A pipeline that accurately recovers T cell receptor (TCR) sequences, including rare TCR sequences, from high throughput sequencing data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines.