humann3 – The Huttenhower Lab

HUMAnN 3.0 (alpha)

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:

And for the time being, if you use HUMAnN 3.0 in your work, please cite:

Franzosa EA*, McIver LJ*, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 15: 962-968 (2018).

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
```

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