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General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, …
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Branch: master

README.md

Michigan Geomicrobiology Lab

Welcome to the GitHub Repo for some general purpose NGS, Data analysis and mining scripts used in the lab. Almost all of them are in core Perl or Python. This means, if you have Perl or Python installed, you won't need anything else to work with these scripts. Please refer to contents.list to find descriptions and location of 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.

This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955.

Language and OS Dependencies

All the scripts have been tested on various flavors of Linux (RHEL5,6; Ubuntu 12.04,14.04; BioLinux5,6,7,8) and Mac OS X. Here is a list of easy to install languages that you'll need:

  • Perl version 5.10 +
  • Python version 2.7 +
  • R version 3 +

Questions/Comments/Beers

  • Sunit Jain, sunitj [AT] umich [DOT] edu (Perl, R, Bash)
  • Daniel Marcus, dnmarc [AT] umich [DOT] edu (Python, Bash)

Principal Investigator

Gregory J. Dick, gdick [AT] umich [DOT] edu


License

All the scripts in the repository here are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Disclaimer

  • Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
  • All the scripts in the repository here 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.

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