Welcome to the GitHub Repo for some general purpose NGS, Data analysis and mining scripts used in the lab. Some scripts implement our short-read QC, assembly, binning, etc. pipeline and depend on the presence of a number of third-party software. The rest are Bash scripts or in core Perl or Python. This means, if you have Perl or Python 3 installed, you won't need anything else to work with these scripts.
Since these scripts are actively being used by the Lab, you can expect full support for any issues. Please do let us know if you find any bugs or easier/quicker/more elegant solutions.
The scripts should work with variuos flavors of Linux and other unix-like environments. Here is a list of easy to install languages that you'll need:
- Perl version 5.10 +
- Python version 3.5 +
- R version 3 +
Please send questions or comments to geo-omics-scripts@umich.edu.
Gregory J. Dick, gdick [AT] umich [DOT] edu
Geo-omics-scripts is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
Geo-omics scripts are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.