Metagenomic Analysis Tools: Difference between revisions
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= Included packages = | = Included packages = | ||
Homepage: https:// | == 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 == | == HUMAnN == | ||
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utility_mapping - full | utility_mapping - full | ||
== | == Kraken 2 == | ||
Version: 1. | Version: 2.1.2 | ||
Homepage: http://ccb.jhu.edu/software/kraken2/ | |||
Database: | |||
Standard Kraken2 database | |||
== MEGAHIT == | |||
Version: 1.2.9 | |||
Homepage: https:// | Homepage: https://github.com/voutcn/megahit | ||
== Metabat == | == Metabat == | ||
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Homepage: https://bitbucket.org/berkeleylab/metabat | Homepage: https://bitbucket.org/berkeleylab/metabat | ||
== 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 | ||
Latest revision as of 19:56, 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
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