The species identification tool can be accessed via the PubMLST RESTful API, allowing it to be incorporated in to an analysis pipeline.
Documentation for the API call can be found at http://bigsdb.readthedocs.io/en/latest/rest.html#db-schemes-scheme-id-sequence.
The following examples assume that you have a FASTA file containing a bacterial genome assembly called contigs.fasta in your current directory.
The curl command can be used to make API calls using the Linux command line access. The FASTA file needs to be base64 encoded and embedded within a JSON payload. This can be done with the following commands.
Output is in JSON format, and looks like the following:
Rank: SPECIES Taxon: Neisseria meningitidis Support: 100% Taxonomy: Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis
Rank: SPECIES Taxon:Neisseria meningitidis Support:100% TaxonomyProteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis