Metagenomic Analysis Tools: Difference between revisions
Jump to navigation
Jump to search
(Add Metagenomic Analysis Tools page) |
(No difference)
|
Revision as of 19:51, 26 May 2021
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
MetaPhlAn
Version: 3.0.9
Homepage: https://huttenhower.sph.harvard.edu/metaphlan/
HUMAnN
Version: 3.0.0
Homepage: https://huttenhower.sph.harvard.edu/humann/
Databases:
chocophlan - full uniref - uniref90_diamond utility_mapping - full
GTDB-Tk
Version: 1.5.0
Homepage: https://ecogenomics.github.io/GTDBTk/index.html
Metabat
Version: 2.12.1
Homepage: https://bitbucket.org/berkeleylab/metabat
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
Kraken 2
Version: 2.1.2
Homepage: http://ccb.jhu.edu/software/kraken2/
Database:
Standard Kraken2 database
CheckM
Version: 1.1.3
Homepage: https://ecogenomics.github.io/CheckM/
MEGAHIT
Version: 1.2.9
Homepage: https://github.com/voutcn/megahit