Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis.
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ABSTRACT:
SUBMITTER: Lee RS
PROVIDER: S-EPMC4922084 | biostudies-literature | 2016 Jul
REPOSITORIES: biostudies-literature
Publications
Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis.
Lee Robyn S RS Behr Marcel A MA
Journal of clinical microbiology 20160413 7
When using genome sequencing for molecular epidemiology, short sequence reads are aligned to an arbitrary reference strain to detect single nucleotide polymorphisms. We investigated whether reference genome selection influences epidemiological inferences of Mycobacterium tuberculosis transmission by aligning sequence reads from 162 closely related lineage 4 (Euro-American) isolates to 7 different genomes. Phylogenetic trees were consistent with use of all but the most divergent genomes, suggesti ...[more]
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