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## Section: New Results

### High-throughtput sequence processing

• Within our collaboration with Montpellier (IRB and LIRMM) we published a paper on CRAC, a software for analysing short RNA sequences and detecting variations among them [5] .

• We have been invited to contribute an invited book chapter on metatranscriptomic data analysis (Methods in Molecular Biology, in press). This chapter covers the complete bioinformatic analysis from raw reads to taxonomic assignation, and introduces our software SortMeRNA (see Paragraph  5.6 ). This is a joint work with team LABIS in Genoscope.

• Evguenia Kopylova defended her thesis on December, the 11th ("New algorithmic and bioinformatic approaches for the analysis of data from high throughput sequencing”, [1] ). The second part of her work deals with a new read mapper for metagenomic sequence data.

• Within our collaboration with the Lille hospital, we developped a seed-based heuristics for the detection of lymphocyte rearrangements from high-throughput data. This method is implemented in the software Vidjil (see Section  5.7 ). Our results were presented at the Jobim conference [8] , and a journal article was submitted.