humann3

HUMAnN 3.0

HUMAnN 3.0 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network. HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data. For more information please see:

User manual || Tutorial || Forum

Citation:

Francesco Beghini1 ,Lauren J McIver2 ,Aitor Blanco-Mìguez1 ,Leonard Dubois1 ,Francesco Asnicar1 ,Sagun Maharjan2,3 ,Ana Mailyan2,3 ,Andrew Maltez Thomas1 ,Paolo Manghi1 ,Mireia Valles-Colomer1 ,George Weingart2,3 ,Yancong Zhang2,3 ,Moreno Zolfo1 ,Curtis Huttenhower2,3 ,Eric A Franzosa2,3 ,Nicola Segata1,4

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife 2021;10:e65088

1 Department CIBIO, University of Trento, Italy
2 Harvard T. H. Chan School of Public Health, Boston, MA, USA
3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA
4 IEO, European Institute of Oncology IRCCS, Milan, Italy

Major updates in v3.0
  • Designed in tandem with MetaPhlAn 3.0.
  • Based on UniProt/UniRef 2019_01 sequences and annotations.
  • Contains 2x more species pangenomes and 3x more gene families (vs. v2.0).
  • Removed version number from executables (just metaphlan and humann now).
Minor updates in v3.0
  • Pangenome sequences must be covered at >50% of sites to be reported (tunable).
  • Additional accuracy and performance re-tuning across all search steps.
  • Translated search updated to use DIAMOND 0.9.
Upcoming changes (post-alpha)
  • Continued documentation updates for v3.0.
    • Most v2.0 documents and instructions still apply in v3.0.
  • Updates to pathway definitions.
    • Currently unchanged from v2.0 (i.e. MetaCyc v19.1).
  • Some HUMAnN helper scripts are unavailable in v3.0 pending updates.
    • E.g. infer_taxonomy
Getting HUMAnN 3.0 (and MetaPhlAn 3.0)
Install via conda
  • (Optionally) Create a new conda environment for the installation
    • conda create --name biobakery3 python=3.7
    • conda activate biobakery3
  • (If you haven't already) Set conda channel priority:
    • conda config --add channels defaults
    • conda config --add channels bioconda
    • conda config --add channels conda-forge
    • conda config --add channels biobakery
  • Install HUMAnN 3.0 software with demo databases:
    • conda install humann -c biobakery
  • Conda-installing HUMAnN 3.0 will automatically install MetaPhlAn 3.0.
    • To install only MetaPhlAn 3.0 execute:
      conda install metaphlan -c bioconda.

Install via pypi
  • pip install humann --no-binary :all:

    The --no-binary :all: parameter will install the pypi package from source. Installing the pypi package from source will also install the required dependencies like bowtie2 and diamond.

Test your installation
    • Run HUMAnN unit tests:
      • humann_test (~1 minute)
    • Run the HUMAnN demo:
      • humann -i demo.fastq -o sample_results
      • Note: MetaPhlAn will fetch and build its marker database during this process, which takes a few minutes (but only has to be done once).
Upgrading your databases
  • The HUMAnN installation comes with small sequence and annotation databases for testing/tutorial purposes.
  • To upgrade your pangenome database:
    • humann_databases --download chocophlan full /path/to/databases --update-config yes
  • To upgrade your protein database:
    • humann_databases --download uniref uniref90_diamond /path/to/databases --update-config yes
  • To upgrade your annotations database:
    • humann_databases --download utility_mapping full /path/to/databases --update-config yes
  • To profile a sample using updated databases:
    • humann -i sample_reads.fastq -o sample_results