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: `DOI:10.5281/zenodo.18770176 `_ 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. Source code: `https://github.com/SMD-Bioinformatics-Lund/bonsai `_ JASEN ^^^^^ JASEN is an upstream sequencing analysis pipeline whose results may be imported into Bonsai and subsequently used by MIMOSA. Source code: `https://github.com/genomic-medicine-sweden/jasen `_ 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 `_