MiSTMiST is a rapid, accurate and flexible (core-genome) MLST allele caller. It can download schemes from EnteroBase, PubMLST (unauthenticated), and cgMLST.org, index them, and query assemblies to call alleles and report (cg)STs, including potential novel alleles.Versions

v1.2.0 (default)

Tags: bioinformatics, MLST, cgMLST, allele calling, typingParameters

INPUT_FASTA (file, multiple) required: FASTA assembly/contigs to type. Provide at least 3 assemblies if you want MiST to also generate phylogeny-ready allele and distance matrices with `mist dists`.

DB (enum) required: Select the indexed MLST/cgMLST database to use for typing. Options: salmonella_cgmlstv2, escherichia_cgmlstv1, listeria_monocytogenes_cgmlst, klebsiella_pneumoniae_complex_cgmlst, serratia_marcescens_cgmlst, acinetobacter_baumannii_cgmlst

min_perc_loci (int): Minimum percentage of loci that should be present in a dataset when generating phylogeny matrices with `mist dists`.

min_perc_samples (int): Minimum percentage of datasets where a locus should be present when generating phylogeny matrices with `mist dists`.

Links

License: GPL-3.0-or-later

Cite as: Bogaerts B, Roosens NHC, et al. MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes. BMC Genomics. doi:10.1186/s12864-025-12324-z

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