Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes

摘要

Comparing strains within the same microbial species has proven effective inthe identification of genes and genomic regions responsible for virulence, aswell as in the diagnosis and treatment of infectious diseases. In this paper,we present Sibelia, a tool for finding synteny blocks in multiple closelyrelated microbial genomes using iterative de Bruijn graphs. Unlike most othertools, Sibelia can find synteny blocks that are repeated within genomes as wellas blocks shared by multiple genomes. It represents synteny blocks in ahierarchy structure with multiple layers, each of which representing adifferent granularity level. Sibelia has been designed to work efficiently witha large number of microbial genomes; it finds synteny blocks in 31 S. aureusgenomes within 31 minutes and in 59 E.coli genomes within 107 minutes on astandard desktop. Sibelia software is distributed under the GNU GPL v2 licenseand is available at: https://github.com/bioinf/Sibelia Sibelia's web-server isavailable at: http://etool.me/software/sibelia