Whole Genome Sequencing of Mycobacterium tuberculosis

WGS was performed as detailed elsewhere (Perez-Lago et al., 2014 (link)) using a HiSeq 2000 device and a Miseq device (Illumina), which generated 101-51–bp paired-end reads. We mapped the reads for each strain using the Burrows-Wheeler Aligner and the ancestral MTB genome as detailed elsewhere (Comas et al., 2013 (link)). SNP calls were made with SAMtools and VarScan (coverage of at least 10×, mean SNP mapping quality of 20). The genome was compared between strains using an in-house script written in R.

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Navarro Y., Pérez-Lago L., Herranz M., Sierra O., Comas I., Sicilia J., Bouza E, & García de Viedma D. (2017). In-Depth Characterization and Functional Analysis of Clonal Variants in a Mycobacterium tuberculosis Strain Prone to Microevolution. Frontiers in Microbiology, 8, 694.

Publication 2017

HiSeq 2000 device Miseq device

Comas Device Genome Strains

Corresponding Organization : Centro de Investigación Biomédica en Red de Enfermedades Respiratorias

Other organizations : Universidad Complutense de Madrid, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Universitat de València, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública

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Variable analysis

independent variables

Sequencing device (HiSeq 2000 and MiSeq, Illumina)

dependent variables

Genomic sequence data (101-51 bp paired-end reads)

control variables

Ancestral Mycobacterium tuberculosis (MTB) genome used as reference for read mapping

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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