HUMAnN protocols

HUMAnN specifications


Unique identifier OMICS_02626
Alternative name The HMP Unified Metabolic Analysis Network
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for The HMP Unified Metabolic Analysis Network

HUMAnN IN pipelines

PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] compared., above, we described a considerable difference in the compositional profiles determined by different species classifiers. hence, we also compared results from super-focus with those from humann2, which is an alternative tool for functional analysis of metagenomes. we observed a similarly pronounced disparity in the results generated by these methods. specifically, 865 level-4 enzyme […]

PMCID: 5589918
PMID: 28883399
DOI: 10.1038/s41598-017-10346-6

[…] species abundances using metaphlan243, and for abundance of uniref gene and kegg orthologs, and functional pathways (metacyc pathways, kegg pathways, and kegg modules) using the software pipeline humann222 and in-house written scripts (available upon request). normalized taxonomic, gene, and pathway abundances were then used for downstream statistical analysis in r. all intestinal microbiome […]

PMCID: 5704459
PMID: 29183332
DOI: 10.1186/s13073-017-0490-5

[…] performed metagenomic sequencing of monthly stool samples from 20 ibd patients and 12 controls (266 total samples). these were taxonomically profiled with metaphlan2 and functionally profiled using humann2. differentially abundant species were identified using maaslin and strain-specific pangenome haplotypes were analyzed using panphlan., we found a significantly higher abundance in patients […]

PMCID: 4791782
PMID: 26975510
DOI: 10.1186/s40168-016-0156-3

[…] reads were also analyzed by metaphlan2 [36] in order to determine the family, genus, and species level relative abundances. diversity was calculated at the genus level with the shannon index. humann version 0.99 [37] was used in conjunction with rapsearch2 [38] and the kegg database [39] to evaluate the presence of the pathway for secondary bile acid biosynthesis (ko00121) […]

PMCID: 3564958
PMID: 22699609
DOI: 10.1038/nature11234

[…] the illumina gaiix platform1. 16s data processing and diversity estimates were performed using qiime27, and metagenomic data were taxonomically profiled using metaphlan13, metabolically profiled by humann26, and assembled for gene annotation and clustering into a unique catalog1. potential pathogens were identified using the patric database14, isolate reference genome annotations drawn […]

HUMAnN institution(s)
The Genome Institute, Washington University School of Medicine, St Louis, MO, USA

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