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What's new in SHAMAN

January 8th 2024 - Sunburst visualization

You can now see the composition of the communities detected in the Network.

December 6th 2023 - Database update

Greengenes2 and unite are up-to-date. New host genomes (mostly mosquitoes) are available.

November 23th 2023 - New data visualization and Global View features

UMAP has been added. We have also updated the Barplot to show other abundances for visualization of the 12 most abundant. For diversity, we have added a visualization of richness with comparison tests.

October 15th 2023 - Updates of PCA and PCoA

These updates bring new data visualizations. We have added some useful features for cluster visualization.

May 9th 2023 - Raw fastq submission is re-activated !

Shaman submission process is up again. We updated in the mean time the unite database to version 9.0.

April 12th 2022 - Improvement of the docker and web interface raw read submission

Raw read submission is now improved for gzip fastq files. We now recommend to send gzip compressed fastq especially for docker instance.

March 11th 2022 - Server maintenance on march 22th

Raw reads submission will be temporarly desactivated from March 22th. For now we keep improving our workflows, submissions from the docker machine should now be much more improved !

February 29th 2022 - Workflow updates

We updated the workflow with Alientrimmer 2 to improve speed and resilience. Let us know if you meet some trouble!

February 29th 2022 - Upgrades on 29 feb !

Raw reads submission will be temporarly desactivated 29 February to upgrade the bioinformatic workflow.

January 13th 2022 - Server maintenance is done

Raw reads submission is back.

January 7th 2022 - Server maintenance from 10-12 January 2021

Raw reads submission will be temporarly desactivated from January 10 until 12 due to a cluster maintenance.

May 5th 2021 - Server maintenance is done

Raw reads submission is back. We updated vsearch to 2.17, RDP classifier to 2.13, Bowtie to and Biom to 2.1.10. Let us know if you meet any issue.

April 28th 2021 - Server maintenance from 3-6 Mai 2021

Raw reads submission will be temporarly desactivated from Mai 3 until 6 due to a cluster maintenance.

Feburary 19th 2020 - New feature

Shaman now support Epi2me data output. Let us know if you meet any issue.

August 19th 2020 - SHAMAN paper is out

We are really happy to announce that the paper describing in depth shaman and comparing this application to other available is out in BMC Bioinformatics. Moreover we keep improving the stability and functions of the application and we hope that we will be able to maintain this application for a long time.

August 14th 2019 - Major update

We performed a global improvement of SHAMAN. The application is now migrated to R 3.6.1. We implemented several visualization for differential analysis and network of abundance. We hope you will enjoy this new version.

April 11th 2019 - Debugging

We fixed few bugs in export system and scatterplot visualisation system.

March 28th 2019 - Packaging

SHAMAN is now available as packrat package. Take a look at download section.

April 17th 2018 - Bioinformatics

The bioinformatic treatment offers a larger access to parameters. We also worked a lot on the documentation.

September 4th 2017 - Bioinformatics

The bioinformatic treatment of fastq reads is now available in SHAMAN. For now, SHAMAN allows to compute OTU, build an OTU table and annotate them with the last version of the available database. This application is for 16S/18S/23S/28S/ITS sequencing.

July 18th 2017 - Normalization and visualisation

A new method for normalization called total counts was added. More options have been added to the abundance tree.

May 30th 2017 - Bug fixes

Some visualization bug with the abundance tree and phylogenetic tree are now fixed. The export of the relative abundance and normalised abundance are now given in the right level. This update prepares the field for the next major release of shaman for June.

March 30th 2017 - Krona, Phylogeny and bug fixes

Krona and phylogenetic tree plots are now available in visualisation. Several new distance are available in PCOA. The import float count matrices is now ok. We have finaly debugged the export of the relative abundance/normalized matrices.

Dec 9th 2016 - Phylogenetic tree and stress plot

You can now upload a phylogenetic tree to calculate the unifrac distance (only available at the OTU level). The stress plot has been added to evaluate the goodness of fit of the NMDS.

Nov 22th 2016 - New visualization and bug fix

We have implemented a new visualization called tree abundance. Some bugs have been fixed (thanks Carine Rey from ENS).

Oct 12th 2016 - Filtering step and bugs fix

You can now apply a filter on the features according to their abundance and the number of samples. Bugs on confidence intervals for the alpha diversity have been fixed.

Sep 21th 2016 - SHAMAN on docker

The install of SHAMAN is now available with docker. The R install is also updated and passed in release candidate state.

Sep 14th 2016 - Download and install SHAMAN

You can install SHAMAN (beta).

Sep 9th 2016 - PCA/PCOA

You can select the axes for the PCOA and PCA plots.

Aug 1st 2016 - Biom format

SHAMAN can now support all the Biom format versions.

Jun 24th 2016 - Comparisons plots

The venn diagram and the heatmap of foldchange have been added to compare the results of 2 or more contrasts.

Jun 17th 2016 - Diversity plots

Enhancement of the visualisation of the diverties. The shanon and inv. shanon have been added.


Read processing

OTU processing

OTU annotation

Directory containing the FastQ files

Match the paired files (only for paired-end sequencing)


Enter the key

Select your file format

Load the count table

Load the taxonomy file

Load the BIOM file

Load the Epi2me file

Load phylogenetic tree (optional)

Experimental design


Size factors

Eigen values

Eigen values


Stress plot

Distance values

Matrix coordinates

Select your plot


Select the modalities







Select your contrast

Reorder data

Plot options

Choose colours
Not significant


Export plot

Regression coefficients

Correlation table

Beta-Gamma values

Richness values

Community table

Select your plot


Select the modalities


Labels options
Margins options


Select your plot


(min = 2)
(between 2 and 4 contrasts)
Select two different contrasts


Labels options
Margins options
Choose colours
Not significant
Significant for contrast 1
Significant for contrast 2
Significant for both contrasts


Export plot

Export table

Export table

Export table

Export table

Krona plot

Click Here!