MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates.

Autor:	Kohl TA; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany., Utpatel C; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany., Schleusener V; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany., De Filippo MR; Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy., Beckert P; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.; German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany., Cirillo DM; Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy., Niemann S; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.; German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
Jazyk:	angličtina
Zdroj:	PeerJ [PeerJ] 2018 Nov 13; Vol. 6, pp. e5895. Date of Electronic Publication: 2018 Nov 13 (Print Publication: 2018).
DOI:	10.7717/peerj.5895
Abstrakt:	Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source. Competing Interests: The authors declare that they have no competing interests.
Databáze:	MEDLINE
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