Software builds for microbiome analysis

[Chromatin15]

Two software tools for multiple labs (Core, Buck, Diaz, Kirkwood) doing microbiome analysis. Humann - https://huttenhower.sph.harvard.edu/humann metaphlan - https://huttenhower.sph.harvard.edu/metaphlan

Easybuilds are available for both.

[dsajdak]

Hi @Chromatin15 Both of these have been installed for avx512 architecture. Please let us know if you need them on older nodes with avx2 CPUs

vortex-future:~$ module spider humann

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  humann: humann/3.6
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    Description:
      HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from
      metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional
      profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the
      question: What are the microbes in my community-of-interest doing (or capable of doing)?

    You will need to load all module(s) on any one of the lines below before the "humann/3.6" module is available to load.

      gcc/11.2.0  openmpi/4.1.1
     This extension is provided by the following modules. To access the extension you must load one of the following modules. Note that any module names in parentheses show the module location in the software hierarchy.

       humann/3.6 (gcc/11.2.0 openmpi/4.1.1)

    This module provides the following extensions:

       humann/3.6 (E)

    Help:

      Description
      ===========
      HUMAnN v3 is a pipeline for efficiently
       and accurately determining the coverage and abundance
       of microbial pathways in a community from metagenomic data.
      Sequencing a metagenome typically produces millions
       of short DNA/RNA reads. This process, referred
       to as functional profiling, aims to describe the metabolic potential
       of a microbial community and its members. More generally,
       functional profiling answers the question:
       What are the microbes in my community-of-interest doing (or capable of doing)?

vortex-future:~$ module spider metaphlan

-----------------------------------------------------------------------------------------------------------------------------------------------------
  metaphlan: metaphlan/4.0.6
-----------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

    Properties:
      Bioinformatic libraries/apps

    You will need to load all module(s) on any one of the lines below before the "metaphlan/4.0.6" module is available to load.

      gcc/11.2.0  openmpi/4.1.1

    This module provides the following extensions:

       hclust2/1.0.0 (E), MetaPhlAn/4.0.6 (E)

    Help:

      Description
      ===========
      MetaPhlAn is a computational tool for profiling the composition
       of microbial communities from metagenomic shotgun sequencing data

      More information
      ================
       - Homepage: https://github.com/biobakery/MetaPhlAn

      Included extensions
      ===================
      hclust2-1.0.0, MetaPhlAn-4.0.6