A simple shell script which access rMLST species identification tool using PubMLST RESTful API.
Only dependencies are curl and jq
git clone https://github.com/Kincekara/rMLST.git
./rmlst.sh contigs.fasta
rmlst.json : A full output of the API as a json file
predicted_taxon.rmlst.txt : A parsed text file including the predicted taxon
A minimal docker (~5.5 MB) is available for containerized applications.
docker pull kincekara/rmlst:0.1
Jolley, K. A., Bliss, C. M., Bennett, J. S., Bratcher, H. B., Brehony, C., Colles, F. M., Wimalarathna, H., Harrison, O. B., Sheppard, S. K., Cody, A. J., & Maiden, M. C. J. (2012). Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology, 158(4), 1005–1015. https://doi.org/10.1099/mic.0.055459-0
RESTful Application Programming Interface (API) — BIGSdb 1.39.0 documentation. (2023). Readthedocs.io. https://bigsdb.readthedocs.io/en/latest/rest.html#db-schemes-scheme-id-sequence
rMLST Species identification via RESTful API. (2020). PubMLST. https://pubmlst.org/species-id/species-identification-via-api