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


ABSTRACT: 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.

SUBMITTER: Kohl TA 

PROVIDER: S-EPMC6238766 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Kohl Thomas Andreas TA   Utpatel Christian C   Schleusener Viola V   De Filippo Maria Rosaria MR   Beckert Patrick P   Cirillo Daniela Maria DM   Niemann Stefan S  

PeerJ 20181113


Analyzing whole-genome sequencing data of <i>Mycobacterium tuberculosis</i> 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 a  ...[more]

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