A method for sequencing a T cell receptor, comprising: a) sequencing short reads of less than about 100 base pairs of RNA obtained from a T cell; b) aligning the short reads with a reference sequence, wherein the reference sequence does not contain a TCR gene sequence, thereby generating a read set comprising mapped short reads and unmapped short reads; c) discarding mapped short reads from the read set; d) assembling the unmapped short reads remaining in the read set into one or more long reads; e) translating the one or more long reads into corresponding amino acid sequences; f) fractioning TCR V region and TCR J region amino acid reference sequences into k-strings of about six amino acids, aligning the k-strings with the corresponding amino acid sequences from step (e), detecting one or more conserved TCR CDR3 residues in the k-strings that map to the corresponding amino acid sequences, scoring the level of conservation detected, and selecting corresponding amino acid sequences with a conservation score above a threshold conservation score, and detecting a candidate CDR3 region amino acid sequence in the selected corresponding amino acid sequences; g) identifying the nucleic acid sequence of the candidate CDR3 region amino acid sequences in the one or more long reads; h) aligning the nucleic acid sequence of the one or more long reads upstream of the candidate CDR3 region nucleic acid sequence with one or more TCR V gene reference sequences, scoring the degree of alignment, and identifying long reads above a threshold alignment score as comprising a candidate TCR V gene sequence; and i) aligning the nucleic acid sequence of the one or more long reads downstream of the candidate CDR3 region nucleic acid sequence with one or more TCR J gene reference sequences, scoring the degree of alignment, and identifying long reads above a threshold alignment score as comprising a candidate TCR J gene sequence, thereby generating a TCR sequence. a) sequencing short reads of less than about 100 base pairs of RNA obtained from a T cell; b) aligning the short reads with a reference sequence, wherein the reference sequence does not contain a TCR gene sequence, thereby generating a read set comprising mapped short reads and unmapped short reads; c) discarding mapped short reads from the read set; d) assembling the unmapped short reads remaining in the read set into one or more long reads; e) translating the one or more long reads into corresponding amino acid sequences; f) fractioning TCR V region and TCR J region amino acid reference sequences into k-strings of about six amino acids, aligning the k-strings with the corresponding amino acid sequences from step (e), detecting one or more conserved TCR CDR3 residues in the k-strings that map to the corresponding amino acid sequences, scoring the level of conservation detected, and selecting corresponding amino acid sequences with a conservation score above a threshold conservation score, and detecting a candidate CDR3 region amino acid sequence in the selected corresponding amino acid sequences; g) identifying the nucleic acid sequence of the candidate CDR3 region amino acid sequences in the one or more long reads; h) aligning the nucleic acid sequence of the one or more long reads upstream of the candidate CDR3 region nucleic acid sequence with one or more TCR V gene reference sequences, scoring the degree of alignment, and identifying long reads above a threshold alignment score as comprising a candidate TCR V gene sequence; and i) aligning the nucleic acid sequence of the one or more long reads downstream of the candidate CDR3 region nucleic acid sequence with one or more TCR J gene reference sequences, scoring the degree of alignment, and identifying long reads above a threshold alignment score as comprising a candidate TCR J gene sequence, thereby generating a TCR sequence.