HUMAnN specifications

Information


Unique identifier OMICS_02626
Name HUMAnN
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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HUMAnN article

HUMAnN citations

 (4)
2018
PMCID: 5915698

[…] were performed with picard and sam tools. functional profiling of high-quality processed reads was facilitated by use of the human microbiome project (hmp) unified metabolic analysis network (humann2 v.0.99) pipeline (55). models of microbial metabolic pathways produced by humann2 were derived from the metacyc database (56) and were the basis for analyses performed on microbial metabolic […]

2017
PMCID: 5532234

[…] and samtools38 and human contamination removed with bmtagger (ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/). subsequently function was assigned to reads using the humann2 suite of tools39; which assigned function based on the chocophlan databases and genes based on uniref40. the humann2 gene abundance table was regrouped using a mapping of go terms […]

2016
PMCID: 4791782

[…] 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) […]

2015
PMCID: 4687345

[…] pattern of functional predictions based on a variety of reference proteins carrying that domain [14, 15]., the three prominent resources for metagenomic data processing (megan [16], mg-rast [17] and humann [18]) all work similarly, aligning translated peptides from the short reads of ngs platforms to databases of well-annotated reference proteins and using single sets of sequence similarity […]

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

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