PT  - JOURNAL ARTICLE
AU  - Peter Javorka
AU  - Vivek Raxwal
AU  - Jan Najvarek
AU  - Karel Riha
TI  - artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
AID  - 10.1101/414433
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 414433
4099  - http://biorxiv.org/content/early/2018/09/12/414433.short
4100  - http://biorxiv.org/content/early/2018/09/12/414433.full
AB  - 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).