A tool for calling the SBT allelic profile of Legionella pneumophila, overcoming multiple copies of mompS
Whole genome sequencing (WGS) has revolutionized the subtyping of Legionella pneumophila but calling the traditional sequence-based type from genomic data is hampered by multiple copies of the mompS locus. We propose a novel bioinformatics solution for rectifying that limitation, ensuring the feasibility of WGS for cluster investigation.
We designed a novel approach based on the alignment of raw reads with a reference sequence. With WGS, reads originating from either of the two mompS copies cannot be differentiated. Therefore, when non-identical copies were present, we applied a read-filtering strategy based on read alignment to a reference sequence via unique 'anchors'. If minimal read coverage was achieved after filtration, a consensus sequence was built based on mapped reads followed by calling the sequence-based typing allele.
mompS is written in Perl and is available both as source code and through a web server.
Use mompS
mompS Web Server
Download mompS from Github
Cite mompS
M. Gordon, E. Yakunin, L. Valinsky, V. Chalifa-Caspi, J. Moran-Gilad, on behalf of the ESCMID Study Group for Legionella Infections (2017) A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era. Clinical Microbiology and Infection 23: 306-310. PMID: 28082190
Contact
Michal Gordon, gordonmi@bgu.ac.il
