Section: New Results

High-throughtput sequence processing

  • Within the PhD of T. T. Tran, we proposed a new indexing structure adapted to GPUs. We studied an indexing scheme with perfect hashing functions, and developed a prototype written in openCL for a read mapper. This read mapper has a sensitivity comparable to state-of-the-art read mappers, and provides substantial time gains in some cases.

  • Within our collaboration with the Lille hospital on the follow-up of leukemia residual disease, we proposed a new heuristic to study immunological VDJ recombinations and follow their evolution along the time. The method is under testing on several datasets obtained from the Ion Torrent sequencer at IRCL (Institut de Recherche sur le Cancer de Lille).

  • Within the PhD of E. Kopylova, we designed an new algorithm to filter out ribosomal RNA sequences from RNA raw data produced in metatranscriptomic sequencing. The method combines text indexing techniques, with the Burst trie, and Universal Levenshtein automaton to allow for seraching with errors. An article has been published the journal Bioinformatics [4] .