Citations

If you use MIMOSA, please cite MIMOSA and the tools it uses for analysis and visualisation.

MIMOSA

Please cite the Zenodo record corresponding to the version of MIMOSA used:

The DOI above always resolves to the latest release. To cite a specific version, use the version-specific DOI listed on the Zenodo record page.

Leaflet

MIMOSA uses Leaflet to provide interactive geographical visualisation of sample locations.

Leaflet — JavaScript library for interactive maps. Source code: https://github.com/Leaflet/Leaflet Project website: https://leafletjs.com

ReporTree

MIMOSA uses ReporTree to perform cgMLST-based tree clustering.

Mixão, V., Pinto, M., Sobral, D. et al. ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Medicine 15, 43 (2023). DOI:10.1186/s13073-023-01196-1

GrapeTree / MSTreeV2

The minimum spanning trees displayed in the MIMOSA dashboard are computed using the MSTreeV2 algorithm implemented in GrapeTree.

Zhou Z, Alikhan NF, Sergeant MJ, et al. GrapeTree: Visualization of core genomic relationships among 100,000+ bacterial pathogens. Genome Research 28(9): 1395–1404 (2018). DOI:10.1101/gr.232397.117

Bonsai

MIMOSA uses Bonsai as its primary source of sample metadata and allele profiles.

JASEN

JASEN is an upstream sequencing analysis pipeline whose results may be imported into Bonsai and subsequently used by MIMOSA.

chewBBACA

Allele profiles imported into MIMOSA are generated by chewBBACA.

Silva M, Machado MP, Silva DN, et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microbial Genomics 4(3): e000166 (2018). DOI:10.1099/mgen.0.000166