Metagenomic Analysis Tools
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
Usage
To utilize these tools, simply put the following two lines in your sbatch job script. Or execute it within the interactive job environment.
module load Anaconda3/2020.11 conda activate metagenomic
Included packages
CheckM
Version: 1.1.3
Homepage: https://ecogenomics.github.io/CheckM/
GTDB-Tk
Version: 1.5.0
Homepage: https://ecogenomics.github.io/GTDBTk/index.html
HUMAnN
Version: 3.0.0
Homepage: https://huttenhower.sph.harvard.edu/humann/
Databases:
chocophlan - full uniref - uniref90_diamond utility_mapping - full
Kraken 2
Version: 2.1.2
Homepage: http://ccb.jhu.edu/software/kraken2/
Database:
Standard Kraken2 database
MEGAHIT
Version: 1.2.9
Homepage: https://github.com/voutcn/megahit
Metabat
Version: 2.12.1
Homepage: https://bitbucket.org/berkeleylab/metabat
MetaPhlAn
Version: 3.0.9
Homepage: https://huttenhower.sph.harvard.edu/metaphlan/
Prokka
Version: 1.14.6
Homepage: https://github.com/tseemann/prokka
Databases:
Kingdoms: Archaea Bacteria Mitochondria Viruses Genera: Enterococcus Escherichia Staphylococcus HMMs: 1-TIGRFAMs_15.0 2-Pfam-A 3-HAMAP HAMAP CMs: Archaea Bacteria Viruses