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
andhumann
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
- E.g.
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
.
- To install only MetaPhlAn 3.0 execute:
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).
-
- Run HUMAnN unit tests:
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
-