humann
Link to section 'Introduction' of 'humann' Introduction
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 check its website: https://huttenhower.sph.harvard.edu/humann/
Link to section 'Versions' of 'humann' Versions
- 3.0.0
- 3.6
Link to section 'Commands' of 'humann' Commands
- humann
- humann3
- humann3_databases
- humann_barplot
- humann_benchmark
- humann_build_custom_database
- humann_config
- humann_databases
- humann_genefamilies_genus_level
- humann_infer_taxonomy
- humann_join_tables
- humann_reduce_table
- humann_regroup_table
- humann_rename_table
- humann_renorm_table
- humann_split_stratified_table
- humann_split_table
- humann_test
- humann_unpack_pathways
Link to section 'Database ' of 'humann' Database
Full ChocoPhlAn, UniRef90, EC-filtered UniRef90, UniRef50, EC-filtered UniRef50, and utility_mapping databases have been downloaded for users.
Link to section 'Module' of 'humann' Module
You can load the modules by:
module load biocontainers
module load humann/3.0.0
Link to section 'Example job' of 'humann' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run HUMAnN3 on our cluster:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=humann
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers humann/3.0.0
# Check the database and config by:
humann_config --print
humann --threads 24 --input examples/demo.fastq --output demo_output --metaphlan-options "--bowtie2db /depot/itap/datasets/metaphlan"