Journal
JOURNAL OF CLINICAL MICROBIOLOGY
Volume 54, Issue 7, Pages 1891-1895Publisher
AMER SOC MICROBIOLOGY
DOI: 10.1128/JCM.00364-16
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- Gouvernement du Canada \ Canadian Institutes of Health Research (CIHR) [125858]
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When using genome sequencing or 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, suggesting that reference choice can be based on considerations other than M. tuberculosis lineage.
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