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artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis

Peter Javorka, Vivek Raxwal, Jan Najvarek, Karel Riha
doi: https://doi.org/10.1101/414433
Peter Javorka
1ARTIN, Bozetechova 19, Brno, Czech Republic
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Vivek Raxwal
2CEITEC, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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  • For correspondence: vivek.raxwal@ceitec.muni.cz karel.riha@ceitec.muni.cz
Jan Najvarek
1ARTIN, Bozetechova 19, Brno, Czech Republic
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Karel Riha
2CEITEC, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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  • For correspondence: vivek.raxwal@ceitec.muni.cz karel.riha@ceitec.muni.cz
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Abstract

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 made 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).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 12, 2018.
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artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
Peter Javorka, Vivek Raxwal, Jan Najvarek, Karel Riha
bioRxiv 414433; doi: https://doi.org/10.1101/414433
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artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
Peter Javorka, Vivek Raxwal, Jan Najvarek, Karel Riha
bioRxiv 414433; doi: https://doi.org/10.1101/414433

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