humann3 – The Huttenhower Lab

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 Maharjan^2,3 ,Ana Mailyan^2,3 ,Andrew Maltez Thomas¹ ,Paolo Manghi¹ ,Mireia Valles-Colomer¹ ,George Weingart^2,3 ,Yancong Zhang^2,3 ,Moreno Zolfo¹ ,Curtis Huttenhower^2,3 ,Eric A Franzosa^2,3 ,Nicola Segata^1,4

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)

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