An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data.

doi:10.1016/j.meegid.2019.104152

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Article

An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases - 1 Apr 2020

Disratthakit Areeya, Toyo-Oka Licht, Thawong Penpitcha, Paiboonsiri Pundharika, Wichukjinda Nuanjun, Ajawatanawong Pravech, Thipkrua Natthakan, Suthum Krairerk, Palittapongarnpim Prasit, Tokunaga Katsushi, Mahasirimongkol Surakameth

Abstract excerpt

Whole-genome sequencing (WGS) data allow for an inference of Mycobacterium tuberculosis (Mtb) clusters by using a pairwise genetic distance of ≤12 single nucleotide polymorphisms (SNPs) as a threshold. However, a problem of discrepancies in numbers of SNPs and genetic distance measurement is a great concern when combining WGS data from different next generation sequencing (NGS) platforms. We performed SNP variant...

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PMID: 31881359
DOI: 10.1016/j.meegid.2019.104152

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PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-07.1.

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