humann3 – The Huttenhower Lab (original) (raw)

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 HUMAnN 3.0

• 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. HUMAnN 2.0).
• Incorporates MetaCyc v24.0 pathway definitions.
• Removed version number from executables (call metaphlan and humann).
• Pangenome sequences must be covered at >50% of sites to be reported (tunable).
• Additional accuracy and performance re-tuning across all search steps.
• Read more in the HUMAnN 3.0 alpha and HUMAnN 3.0 release notes.

Additional updates (including minor releases)

• The functionality of the humann_infer_taxonomy helper script (which assigns putative taxonomy to unclassified UniRef abundance) has been improved using new error-corrected UniRef LCA definitions.
• The humann_barplot helper script has been redesigned to label more community species and to facilitate cross-plot consistency.
• The HUMAnN command-line interface has been reorganized to group together related arguments (e.g. all arguments related to translated search).
• HUMAnN 3.1 implemented further refinements to the pangenome catalog.
• HUMAnN 3.5 implemented forward compatibility with MetaPhlAn 4 taxonomic profiles.
• HUMAnN 3.6 fixed a critical error caused by DIAMOND 0.9.36 that resulted in loss of translated alignments.

Getting HUMAnN 3.0 (and MetaPhlAn 3.0)

• (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.

• ```

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.

* * 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)_.

* 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
  ```