SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

BMC Bioinformatics

Table 1 Mapping SHAMAN among the other web interface for metataxonomic analysis

Category	SHAMAN	ASaiM	FROGS	MetaDEGalaxy	Qiita	Shiny-phyloseq	Metaviz	Vamps
OTU processing	Yes	Yes	Yes	Yes	Yes	No	No	No
Computation time (min)	60	>1day	208	>1day	303	NR	NR	NR
Normalization	Yes	No	Yes	Yes	No	No	No	No
Modelling	Yes	No	Manova	Yes	No	D	M	No
Diversity analysis	Yes	No	Yes	Yes	Yes	Alpha	Alpha	Alpha
Phylogenetic analysis	Yes	No	Yes	Yes	Yes	Yes	No	Tree
Feature abundance plots	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Ordination plots	Yes	No	Yes	No	Yes	Yes	Yes	Yes
Network plots	Yes	No	No	Yes	No	Yes	No	Yes
World-map distribution	No	No	No	No	No	No	No	Yes
Statistics plots	Yes	NR	No	No	NR	Yes	NR	NR
Interactive visualization	31	1	2;P	6	3	8	9	17
Raw data storage	No	No	No	No	Yes	No	No	Yes
Result storage	Yes	No	No	No	Yes	No	No	Yes
Online web Interface	Yes	No	No	Yes	Yes	No	Yes	Yes
R packaging	No	NR	NR	NR	NR	Yes	Yes	NR
Docker	Yes	Yes	No	No	No	No	Yes	No
Conda	Yes	No	Yes	No	Yes	No	Yes	No

D: Export from DESeq2, M: Export from Metagenomeseq, NR: Non relevant feature, P: Import/Export to Phyloseq, Computation time is indicated for the OTU processing of the Zymo mock communities, Number of unique interactive visualization are reported for each web interface in section ‘Interactive visualization’. We reported a specific implementation with the following terms: Alpha indicates when only alpha diversity is available for diversity analysis, Manova is indicated for FROGS because differential abundant features are detected with a Manova instead of a General Linearized Model. Tree indicates when no unifrac distance is available after computing the phylogeny of the OTUs

ISSN: 1471-2105