artMAP, TeloTool and others.. please scroll
artMAP is a user friendly tool to analyze next generation sequencing data generated from the forward genetic screen in Arabidopsis. artMAP provides a graphical user interface and can be run on a regular laptop and desktop without the need of bioinformatics expertise. artMAP can process input sequencing files generated from single or paired-end sequencing in BAM or FASTQ format. 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 the artMAP is available on github (https://github.com/RihaLab/artMAP).
artMAP can be installed in 4 easy steps
1) First, install Docker on your computer. Docker can be installed from https://docs.docker.com/install/
2) Another requirement for running the artMAP is docker-compose. For Mac and Windows, docker-compose is a part of docker installation. However, for Linux, you need to install it from https://docs.docker.com/compose/install/.
3) Place the docker-compose.yml file (https://github.com/RihaLab/artMAP) in the desired folder from where you want to run artMAP.
4) Finally, to run artMAP open your command prompt and navigate to the folder where the docker-compose.yml file is placed. Next, type docker-compose up which will pull the artMAP and run it on port 3000. Now the tool is accessible on http://localhost:3000
More information is available in the supplementary information of the article (https://www.biorxiv.org/content/early/2018/09/12/414433)
Please cite the article if use artMAP for you research
artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
Peter Javorka, Vivek Kumar Raxwal, Jan Najvarek, Karel Riha
bioRxiv 414433; doi: https://doi.org/10.1101/414433
artMAP is built in collaboration with ARTIN (https://www.artinsolutions.com/)
In case of any query, you can write us
Peter Javorka : peter.javorka@artin.cz
Vivek Raxwal : vivek.raxwal@ceitec.muni.cz
Karel Riha: Karel.riha@ceitec.muni.cz
TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction
This program provides a standardized mean for quick and reliable extraction of quantitative data from TRF autoradiograms; its wide application will allow accurate comparison between datasets generated in different laboratories.
See here.
