https://github.com/geo-omics/scripts
Metagenomic pipeline and other general scripts used in the lab.
https://github.com/geo-omics/scripts
geomicrobiology microbiology ngs-analysis perl python umich
Last synced: 8 months ago
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Metagenomic pipeline and other general scripts used in the lab.
- Host: GitHub
- URL: https://github.com/geo-omics/scripts
- Owner: Geo-omics
- License: gpl-3.0
- Created: 2013-04-26T16:27:16.000Z (about 13 years ago)
- Default Branch: master
- Last Pushed: 2025-01-24T19:22:10.000Z (over 1 year ago)
- Last Synced: 2025-09-05T19:33:37.121Z (10 months ago)
- Topics: geomicrobiology, microbiology, ngs-analysis, perl, python, umich
- Language: Perl
- Homepage: https://sites.lsa.umich.edu/geomicro/
- Size: 11.1 MB
- Stars: 36
- Watchers: 7
- Forks: 22
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: COPYING
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README
# Michigan Geomicrobiology Lab
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](http://www.perl.org/ "Perl Home") or [Python](https://www.python.org/
"Python Home"). 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](https://github.com/Geo-omics/scripts/issues "Report an
issue"). Please do let us know if you find any bugs or easier/quicker/more
elegant solutions.
## Language and OS Dependencies
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 +
## Contact
Please send questions or comments to .
## Principal Investigator
[Gregory J. Dick](https://sites.lsa.umich.edu/geomicro/ "Geomicrobiology Lab Homepage"), gdick [AT] umich [DOT] edu
## License
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.
## Disclaimer
**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.**