Ségolène Caboche
Lille University of Science and Technology, France
Title: A pipeline to quickly and automatically characterize microbial genomes from high-throughput sequencing data
Biography
Biography: Ségolène Caboche
Abstract
Recent advances in high-throughput sequencing (HTS) technologies open new perspectives in diagnostic microbiology (management of infected patients) and in epidemiology of infectious diseases. The Whole-Genome Sequencing application has significantly increased our knowledge of microorganism genomes and has facilitated investigations in clinical microbiology, but from concept to routine use, some bottlenecks still need to be unlocked. One of these is the step of data analysis which requires bioinformatic expertise, needs to be reproducible and is often time consuming. Here we present MICRA, a freely available on-line pipeline to quickly and automatically characterize microbial genomes from HTS data. MICRA requires only the raw sequencing data (fastq) as input and then automatically finds the most closely related genomes based on sequence similarity (called reference genomes) and establish lists of discrepancies in term of genes and plasmids content and in term of variations compared to reference genomes. Optional modules allows the user to obtain Venn diagrams to quickly compare the gene content and/or the variations list between several strains. Another module identifies drug susceptibility and resistance genes and generates an e-antibiogram of the analyzed strain. All the steps included in MICRA were optimized in time. For example, for a PGM Ion Torrent run containing more than 2 million of 200-bases reads, the pipeline requires only 15 minutes to generate a full analysis. Diagnostic microbiology and epidemiology of infectious diseases, will benefit from such pipeline as it defines a new standard of genome-based diagnosis combining results from a former time-consuming and heterogeneous multiple step method.