We develop an algorithm to process high-throughput sequencing data to detect sequences with V(D)J recombinations as well as incomplete or uncommon recombinations. We gather these sequences into clonotypes.
We use and improve state-of-the-art text algorithms (spaced seeds, automata, bit parallelism, indexing structures...) to provide efficient analytical methods. As fat as possible, we do not compute full alignments. We always plan to improve the algorithm, improving accuracy and speed and providing more pertinent analysis for immunology and hematology. We benchmark and improve the algorithm on carefully curated sequences.