Informace o publikaci

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

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JAVORKA P. RAXWAL Vivek Kumar NAJVAREK J. ŘÍHA Karel

Rok publikování 2019
Druh Článek v odborném periodiku
Časopis / Zdroj PLANT DIRECT
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146
Doi http://dx.doi.org/10.1002/pld3.146
Klíčová slova Arabidopsis thaliana; bioinformatics; de novo mutation; ethyl methanesulfonate; forward genetic screen; mapping-by-sequencing
Popis 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).
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