Metagenomic Analysis Tools

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Attention: Research Computing Documentation has Moved
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