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@article{1641557,
author = {Javorka, P. and Raxwal, Vivek Kumar and Najvarek, J. and Říha, Karel},
article_location = {CHICHESTER},
article_number = {6},
doi = {http://dx.doi.org/10.1002/pld3.146},
keywords = {Arabidopsis thaliana; bioinformatics; de novo mutation; ethyl methanesulfonate; forward genetic screen; mapping-by-sequencing},
language = {eng},
issn = {2475-4455},
journal = {PLANT DIRECT},
title = {artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis},
url = {https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146},
volume = {3},
year = {2019}
}
TY - JOUR
ID - 1641557
AU - Javorka, P. - Raxwal, Vivek Kumar - Najvarek, J. - Říha, Karel
PY - 2019
TI - artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis
JF - PLANT DIRECT
VL - 3
IS - 6
SP - 1-7
EP - 1-7
PB - JOHN WILEY & SONS LTD
SN - 24754455
KW - Arabidopsis thaliana
KW - bioinformatics
KW - de novo mutation
KW - ethyl methanesulfonate
KW - forward genetic screen
KW - mapping-by-sequencing
UR - https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146
L2 - https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146
N2 - 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).
ER -
JAVORKA, P., Vivek Kumar RAXWAL, J. NAJVAREK and Karel ŘÍHA. artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis. \textit{PLANT DIRECT}. CHICHESTER: JOHN WILEY \&{}amp; SONS LTD, 2019, vol.~3, No~6, p.~1-7. ISSN~2475-4455. Available from: https://dx.doi.org/10.1002/pld3.146.
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