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

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...

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Autores principales: Xia, Eryu, Teo, Yik-Ying, Ong, Rick Twee-Hee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756441/
https://www.ncbi.nlm.nih.gov/pubmed/26883915
http://dx.doi.org/10.1186/s13073-016-0270-7
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author Xia, Eryu
Teo, Yik-Ying
Ong, Rick Twee-Hee
author_facet Xia, Eryu
Teo, Yik-Ying
Ong, Rick Twee-Hee
author_sort Xia, Eryu
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0270-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-47564412016-02-18 SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads Xia, Eryu Teo, Yik-Ying Ong, Rick Twee-Hee Genome Med Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0270-7) contains supplementary material, which is available to authorized users. BioMed Central 2016-02-17 /pmc/articles/PMC4756441/ /pubmed/26883915 http://dx.doi.org/10.1186/s13073-016-0270-7 Text en © Xia et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Xia, Eryu
Teo, Yik-Ying
Ong, Rick Twee-Hee
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title_full SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title_fullStr SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title_full_unstemmed SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title_short SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
title_sort spotyping: fast and accurate in silico mycobacterium spoligotyping from sequence reads
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756441/
https://www.ncbi.nlm.nih.gov/pubmed/26883915
http://dx.doi.org/10.1186/s13073-016-0270-7
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