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Metagenomic Analysis Tools

From UABgrid Documentation

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= Included packages =
 
= Included packages =
== MetaPhlAn ==
 
Version: 3.0.9
 
  
Homepage: https://huttenhower.sph.harvard.edu/metaphlan/
+
== CheckM ==
 +
Version: 1.1.3
 +
 
 +
Homepage: https://ecogenomics.github.io/CheckM/
 +
 
 +
== GTDB-Tk ==
 +
Version: 1.5.0
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 +
Homepage: https://ecogenomics.github.io/GTDBTk/index.html
  
 
== HUMAnN ==
 
== HUMAnN ==
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   utility_mapping - full
 
   utility_mapping - full
  
== GTDB-Tk ==
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== Kraken 2 ==
Version: 1.5.0
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Version: 2.1.2
  
Homepage: https://ecogenomics.github.io/GTDBTk/index.html
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Homepage: http://ccb.jhu.edu/software/kraken2/
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Database:
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  Standard Kraken2 database
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== MEGAHIT ==
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Version: 1.2.9
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Homepage: https://github.com/voutcn/megahit
  
 
== Metabat ==
 
== Metabat ==
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Homepage: https://bitbucket.org/berkeleylab/metabat
 
Homepage: https://bitbucket.org/berkeleylab/metabat
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 +
== MetaPhlAn ==
 +
Version: 3.0.9
 +
 +
Homepage: https://huttenhower.sph.harvard.edu/metaphlan/
  
 
== Prokka ==
 
== Prokka ==
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   HMMs: 1-TIGRFAMs_15.0 2-Pfam-A 3-HAMAP HAMAP
 
   HMMs: 1-TIGRFAMs_15.0 2-Pfam-A 3-HAMAP HAMAP
 
   CMs: Archaea Bacteria Viruses
 
   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
 

Latest revision as of 14:56, 26 May 2021

Contents


[edit] 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

[edit] Included packages

[edit] CheckM

Version: 1.1.3

Homepage: https://ecogenomics.github.io/CheckM/

[edit] GTDB-Tk

Version: 1.5.0

Homepage: https://ecogenomics.github.io/GTDBTk/index.html

[edit] HUMAnN

Version: 3.0.0

Homepage: https://huttenhower.sph.harvard.edu/humann/

Databases:

 chocophlan - full
 uniref - uniref90_diamond
 utility_mapping - full

[edit] Kraken 2

Version: 2.1.2

Homepage: http://ccb.jhu.edu/software/kraken2/

Database:

 Standard Kraken2 database

[edit] MEGAHIT

Version: 1.2.9

Homepage: https://github.com/voutcn/megahit

[edit] Metabat

Version: 2.12.1

Homepage: https://bitbucket.org/berkeleylab/metabat

[edit] MetaPhlAn

Version: 3.0.9

Homepage: https://huttenhower.sph.harvard.edu/metaphlan/

[edit] 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