Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis
2016 ◽
Vol 54
(7)
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pp. 1891-1895
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Keyword(s):
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 ofMycobacterium tuberculosistransmission 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 thanM. tuberculosislineage.
2016 ◽
Vol 54
(7)
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pp. 1862-1870
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2015 ◽
Vol 54
(3)
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pp. 779-781
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2016 ◽
Vol 54
(12)
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pp. 2969-2974
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2014 ◽
Vol 80
(14)
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pp. 4398-4413
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2013 ◽
Vol 57
(11)
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pp. 5658-5664
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