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SimulaTE: simulating complex landscapes of transposable elements of populations

MOTIVATION: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. RESULT...

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Detalles Bibliográficos
Autor principal: Kofler, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905622/
https://www.ncbi.nlm.nih.gov/pubmed/29186298
http://dx.doi.org/10.1093/bioinformatics/btx772
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author Kofler, Robert
author_facet Kofler, Robert
author_sort Kofler, Robert
collection PubMed
description MOTIVATION: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. RESULTS: To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. AVAILABILITY AND IMPLEMENTATION: SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation.
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spelling pubmed-59056222018-04-23 SimulaTE: simulating complex landscapes of transposable elements of populations Kofler, Robert Bioinformatics Applications Notes MOTIVATION: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. RESULTS: To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. AVAILABILITY AND IMPLEMENTATION: SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation. Oxford University Press 2018-04-15 2017-11-27 /pmc/articles/PMC5905622/ /pubmed/29186298 http://dx.doi.org/10.1093/bioinformatics/btx772 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Kofler, Robert
SimulaTE: simulating complex landscapes of transposable elements of populations
title SimulaTE: simulating complex landscapes of transposable elements of populations
title_full SimulaTE: simulating complex landscapes of transposable elements of populations
title_fullStr SimulaTE: simulating complex landscapes of transposable elements of populations
title_full_unstemmed SimulaTE: simulating complex landscapes of transposable elements of populations
title_short SimulaTE: simulating complex landscapes of transposable elements of populations
title_sort simulate: simulating complex landscapes of transposable elements of populations
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905622/
https://www.ncbi.nlm.nih.gov/pubmed/29186298
http://dx.doi.org/10.1093/bioinformatics/btx772
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