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

J 2019

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

JAVORKA, P., Vivek Kumar RAXWAL, J. NAJVAREK a Karel ŘÍHA

Základní údaje

Originální název

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

Autoři

JAVORKA, P., Vivek Kumar RAXWAL (356 Indie, domácí), J. NAJVAREK a Karel ŘÍHA (203 Česká republika, garant, domácí)

Vydání

PLANT DIRECT, CHICHESTER, JOHN WILEY & SONS LTD, 2019, 2475-4455

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.725

Kód RIV

RIV/00216224:14740/19:00108223

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/pld3.146

UT WoS

000509900300003

Klíčová slova anglicky

Arabidopsis thaliana; bioinformatics; de novo mutation; ethyl methanesulfonate; forward genetic screen; mapping-by-sequencing

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 1. 4. 2020 12:08, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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).

Návaznosti

EF15_003/0000479, projekt VaV

Název: Regulace rostlinné meiózy

GA16-18578S, projekt VaV

Název: Funkce UPF1 helikázy v procesech odehrávajících se v buněčném jádře

Investor: Grantová agentura ČR, Funkce UPF1 helikázy v procesech odehrávajících se v buněčném jádře

Citovat

JAVORKA, P., Vivek Kumar RAXWAL, J. NAJVAREK a Karel ŘÍHA. artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis. PLANT DIRECT. CHICHESTER: JOHN WILEY & SONS LTD, 2019, roč. 3, č. 6, s. 1-7. ISSN 2475-4455. Dostupné z: https://dx.doi.org/10.1002/pld3.146.

@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 a 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, roč.~3, č.~6, s.~1-7. ISSN~2475-4455. Dostupné z: https://dx.doi.org/10.1002/pld3.146.

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