artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F19%3A00108223" target="_blank" >RIV/00216224:14740/19:00108223 - isvavai.cz</a>
Result on the web
<a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146" target="_blank" >https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/pld3.146" target="_blank" >10.1002/pld3.146</a>

Result language
angličtina
Original language name
artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis
Original language description
Mapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP makes the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10611 - Plant sciences, botany

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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