artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis
Identifikátory výsledku
Kód výsledku v IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F19%3A00108223" target="_blank" >RIV/00216224:14740/19:00108223 - isvavai.cz</a>
Výsledek na webu
<a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146" target="_blank" >https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pld3.146</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/pld3.146" target="_blank" >10.1002/pld3.146</a>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis
Popis výsledku v původním jazyce
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).
Název v anglickém jazyce
artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis
Popis výsledku anglicky
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).
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10611 - Plant sciences, botany
Návaznosti výsledku
Projekt
Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.
Návaznosti
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Ostatní
Rok uplatnění
2019
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
PLANT DIRECT
ISSN
2475-4455
e-ISSN
—
Svazek periodika
3
Číslo periodika v rámci svazku
6
Stát vydavatele periodika
GB - Spojené království Velké Británie a Severního Irska
Počet stran výsledku
7
Strana od-do
1-7
Kód UT WoS článku
000509900300003
EID výsledku v databázi Scopus
2-s2.0-85068070825