TB-ANNOTATOR: A scalable web application that allows in-depth analysis of very large sets of publicly available Mycobacterium tuberculosis complex genomes
Résumé
Tuberculosis continues to be one of the most threatening bacterial
diseases in the world. Since the beginning of the NGS era, there are
more than 160,000 Short Read Archives (SRAs) of Mycobacterium
tuberculosis complex in the databases. Gathering this high amount of
data could help better understanding this bacterium and fighting against
tuberculosis. In addition, after gathering, it is important to be able
to study, in its entirety and in-depth, this important mass of data. We
developed the “TB-Annotator” web application that combines a database
containing at the time of writing 102,000 SRAs (after checking their
quality). We present a fully featured analysis platform to explore and
query such a large amount of data. The objective is to present this
platform tool centered on the key notion of exclusivity, to show its
numerous capacities (detection of single nucleotide variants, insertion
sequences, deletion regions, spoligotyping, etc.) and its general
functioning. We compared TB-Annotator to existing platform tools for the
study of tuberculosis, and showed that its objectives are original and
have no equivalent at present. The database on which it is based will be
presented, with the numerous advanced search queries and screening
capacities it offers, and the interest and originality of its
phylogenetic tree navigation interface will be detailed. We will end
this presentation with examples of the results made possible by
TB-Annotator, followed by avenues for future improvement.