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:
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
- 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.
- 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.
- (Optionally) Create a new conda environment for the installation
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conda create --name biobakery3 python=3.7
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conda activate biobakery3
-
- (If you haven't already) Set conda channel priority:
-
conda config --add channels defaults
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conda config --add channels bioconda
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conda config --add channels conda-forge
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conda config --add channels biobakery
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- 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:
-
pip install humann --no-binary :all:
The
--no-binary :all:
parameter will install thepypi
package fromsource
. Installing thepypi
package fromsource
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).
-
- Run HUMAnN unit tests:
- 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:
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humann_databases --download uniref uniref90_diamond /path/to/databases --update-config yes
-
- To upgrade your annotations database:
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humann_databases --download utility_mapping full /path/to/databases --update-config yes
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- To profile a sample using updated databases:
-
humann -i sample_reads.fastq -o sample_results
-