nomenclature is a tool nested within CRobot platform and can handle all the requests from EnteroBase website or from EnteroTools pipelines. It is currently store all the MLST information by itself but will become a API wrapper of NServ in V3.0. It can be called independently and is generally run (for each available genotyping scheme) after the QAssembly pipeline, which offers an automatic solution from short reads to MLST typing. (Current version is v.3.2 - various information may be out of date.)

(?? Current Version: 2.0

Developing Version: 3.0

nomenclature V3.0 will not store MLST information and only pass the assemblies onto NServ. NServ, as a standalone server, will handle all the MLST typing and synchronization with website. )

Inputs/Outputs

Parameters

{
    "params": {
        "scheme": "Senteria_UoW",        # Ecoli_UoW, Yersinia_UoW, Mcatarrhalis_UoW
        "genome_id": "SAL_AA0001AA_AS"
    },
    "inputs": {
        "genome_seq": "SAL_AA0001AA_AS.scaffold.fastq"
    }
}

Output fields

{
    "log": "A JSON string describes alleles and STs"
}

History

Version 3.0

??

Version 2.0

Starts to call new ST types from MLST UoW.

Version 1.0

Serves new allele callings from MLST UoW.