SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads

Genome Medicine
Eryu XiaRick Twee-Hee Ong

Abstract

SpoTyping is a fast and accurate program for in silico spoligotyping of Mycobacterium tuberculosis isolates from next-generation sequencing reads. This novel method achieves high accuracy for reads of both uniform and varying lengths, and is about 20 to 40 times faster than SpolPred. SpoTyping also integrates the function of producing a report summarizing associated epidemiological data from a global database of all isolates having the same spoligotype. SpoTyping is freely available at: https://github.com/xiaeryu/SpoTyping-v2.0 .

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Citations

May 19, 2016·Emerging Infectious Diseases·Igor MokrousovOlga Narvskaya
Oct 23, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Kiatichai FaksriRick Twee-Hee Ong
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Datasets Mentioned

BETA
ERP006354

Methods Mentioned

BETA
genotyping
electrophoresis

Software Mentioned

Velvet
CASTB
Mac
FASTQ
Windows
Excel
Fedora Linux
R script
OS
Linux

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