Mobster: accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in...

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Autores principales: Thung, Djie Tjwan, de Ligt, Joep, Vissers, Lisenka EM, Steehouwer, Marloes, Kroon, Mark, de Vries, Petra, Slagboom, Eline P, Ye, Kai, Veltman, Joris A, Hehir-Kwa, Jayne Y
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228151/
https://www.ncbi.nlm.nih.gov/pubmed/25348035
http://dx.doi.org/10.1186/s13059-014-0488-x
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author Thung, Djie Tjwan
de Ligt, Joep
Vissers, Lisenka EM
Steehouwer, Marloes
Kroon, Mark
de Vries, Petra
Slagboom, Eline P
Ye, Kai
Veltman, Joris A
Hehir-Kwa, Jayne Y
author_facet Thung, Djie Tjwan
de Ligt, Joep
Vissers, Lisenka EM
Steehouwer, Marloes
Kroon, Mark
de Vries, Petra
Slagboom, Eline P
Ye, Kai
Veltman, Joris A
Hehir-Kwa, Jayne Y
author_sort Thung, Djie Tjwan
collection PubMed
description Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-42281512014-11-13 Mobster: accurate detection of mobile element insertions in next generation sequencing data Thung, Djie Tjwan de Ligt, Joep Vissers, Lisenka EM Steehouwer, Marloes Kroon, Mark de Vries, Petra Slagboom, Eline P Ye, Kai Veltman, Joris A Hehir-Kwa, Jayne Y Genome Biol Method Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users. BioMed Central 2014-10-28 2014 /pmc/articles/PMC4228151/ /pubmed/25348035 http://dx.doi.org/10.1186/s13059-014-0488-x Text en © Thung et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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 Method
Thung, Djie Tjwan
de Ligt, Joep
Vissers, Lisenka EM
Steehouwer, Marloes
Kroon, Mark
de Vries, Petra
Slagboom, Eline P
Ye, Kai
Veltman, Joris A
Hehir-Kwa, Jayne Y
Mobster: accurate detection of mobile element insertions in next generation sequencing data
title Mobster: accurate detection of mobile element insertions in next generation sequencing data
title_full Mobster: accurate detection of mobile element insertions in next generation sequencing data
title_fullStr Mobster: accurate detection of mobile element insertions in next generation sequencing data
title_full_unstemmed Mobster: accurate detection of mobile element insertions in next generation sequencing data
title_short Mobster: accurate detection of mobile element insertions in next generation sequencing data
title_sort mobster: accurate detection of mobile element insertions in next generation sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228151/
https://www.ncbi.nlm.nih.gov/pubmed/25348035
http://dx.doi.org/10.1186/s13059-014-0488-x
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