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artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
- Publication Year :
- 2018
- Publisher :
- Cold Spring Harbor Laboratory, 2018.
-
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 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).
- Subjects :
- Source code
Ethyl methanesulfonate
Computer science
media_common.quotation_subject
medicine.disease_cause
Machine learning
computer.software_genre
Genome
03 medical and health sciences
chemistry.chemical_compound
0302 clinical medicine
medicine
030304 developmental biology
media_common
0303 health sciences
Mutation
User Friendly
business.industry
Plant biology
Pipeline (software)
Identification (information)
chemistry
Container (abstract data type)
Arabidopsis genome
Artificial intelligence
business
computer
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....4591f258b2d574071b687df22801bb6e
- Full Text :
- https://doi.org/10.1101/414433