mlsttype

MLSType from Enterobase Tool Kit (EToKi).

EToKi MLSType identities allelic sequences in a queried genome, by comparing it with the exemplar alleles generated by MLSTdb. It requires USEARCH (GPLv3) and BLAST (Public domain). Like the original package, this one is also released under GPLv3.

Calculate cgMLST genotype for a queried genome and print to standard output

python mlstype/MLSType.py -i examples/SAL_QD2830AA_AS.result.fasta.gz \
-r examples/cgMLST_v2_ref.fasta.gz -k cgmlst_SAL -o STDOUT

Citation

Zhou Z, Alikhan NF, Mohamed K, Fan Y; Agama Study Group; Achtman M. The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020 Jan;30(1):138-152. doi: 10.1101/gr.251678.119. Epub 2019 Dec 6. PMID: 31809257; PMCID: PMC6961584.