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Section: Application Domains

Sequence processing for Next Generation Sequencing

As said in the introduction of this document, biological sequence analysis is a foundation subject for the team. In the last years, sequencing techniques have experienced remarkable advances with Next Generation Sequencing (NGS), that allow for fast and low-cost acquisition of huge amounts of sequence data, and outperforms conventional sequencing methods. These technologies can apply to genomics, with DNA sequencing, as well as to transcriptomics, with RNA sequencing. They promise to address a broad range of applications including: Comparative genomics, individual genomics, high-throughput SNP detection, identifying small RNAs, identifying mutant genes in disease pathways, profiling transcriptomes for organisms where little information is available, researching lowly expressed genes, studying the biodiversity in metagenomics. From a computational point of view, NGS gives rise to new problems and gives new insight on old problems by revisiting them: Accurate and efficient remapping, pre-assembling, fast and accurate search of non exact but quality labelled reads, functional annotation of reads, ...