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Metagenomic Analysis Tools

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Hello UAB Research Computing Community!


We have created a new streamlined and user-friendly set of documentation for our services. Please visit https://uabrc.github.io/ for our new documentation site. Please bear in mind the documentation is still a work in progress and subject to change.


As part of the process we are deprecating, and eventually retiring, the current documentation site here at https://docs.uabgrid.uab.edu/.


Thank you for your continued use and support.


The Research Computing Team

Contents


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