ArtMAP: A user‐friendly tool for mapping ethyl methanesulfonate‐induced mutations in Arabidopsis. (11th June 2019)

• Record Type: Journal Article
• Authors: Javorka, Peter; Raxwal, Vivek K.; Najvarek, Jan; Riha, Karel
• Is Part Of: Plant direct. Volume 3:Number 6(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-06-11
• Subjects: Arabidopsis thaliana -- bioinformatics -- de novo mutation -- ethyl methanesulfonate -- forward genetic screen -- mapping‐by‐sequencing; Plants -- Periodicals; Botany -- Periodicals; 571.205
• DOI: 10.1002/pld3.146
• Languages: English
• ISSNs: 2475-4455

Abstract

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 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 ).