gian77 / metagaap

metaGenome Assembly and Annotation Pipeline

metaGAAP

metaGAAP v. 1.0 - metaGenome Assembly and Annotation Pipeline

This piepeline is under development, please, be patient!

To clone this repo

git clone [email protected]:Gian77/metaGAAP.git

NOTE
This pipeline was born for running on the HPCC at Michigan State University which run the SLURM (Simple Linux Utility for Resource Management) job scheduler system. If you want to run this piepline in any other systems it will require substantial modification of the main, as well as, the accessory scripts.

This pipeline is based upon work supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-SC0018409

Software needed to fully run metaGAAP on HPCC

Please install via conda (or use the binaries in the HPPC) of all these software below.

• FastQC

• quast

• Kraken 2

• Bracken

• CheckM

• R

Acknowledgements

Gian M.N. Benucci <benucci[at]msu[dot]edu> work was suppeorted by GLBRC (Great Lakes Bioenergy Research Center).