Computational protocol: In-Depth Characterization and Functional Analysis of Clonal Variants in a Mycobacterium tuberculosis Strain Prone to Microevolution

Similar protocols

Protocol publication

[…] WGS was performed as detailed elsewhere (Perez-Lago et al., ) 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., ). 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. […]

Pipeline specifications

Software tools BWA, SAMtools, VarScan
Application WGS analysis
Organisms Homo sapiens
Diseases Infection, Tuberculosis
Chemicals Nucleotides