clonotypeR

clonotypeR processes and quantitatively analyzes millions of V-CDR3-J clonotypes from Illumina short-read sequencing data to identify and enumerate T-cell receptor (TcR) V-CDR3-J combinations.

Key Features:

• Five-item unique identifier: Uses a novel five-item identifier system to uniquely and unambiguously define each TcR sequence at the V-CDR3-J level.
• Finite-state automaton mapping: Applies a finite-state automaton to map Illumina short-read sequence data for individual TcRs to their respective identifiers.
• Error handling with mismatch tolerance: Extends the mapping algorithm to accommodate single-base pair mismatches and reports maintained accuracy (>88%) with up to 1% error in in silico sequences.
• High-performance assignment: Assigns sequences at a rate more than two orders of magnitude faster than classical pairwise alignment algorithms.
• Implementation: Implemented in Python (v2.6).

Scientific Applications:

• Antigen-specific receptor repertoire analysis: Enables quantitative analysis of antigen-specific TcR repertoires across large sequencing libraries.
• T-cell diversity and immune response study: Provides data to investigate T-cell diversity and mechanisms of immune responses.
• V and J usage bias analysis: Supports exploration of V and J usage biases within human peripheral blood repertoires independent of antigen exposure.

Methodology:

Mapping Illumina short reads to five-item TcR identifiers using a finite-state automaton with an extension to allow single-base mismatches, and validation on artificial in silico sequences and published human TcR-β sequences.