Metagenomic Analysis Tools

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