An implementation of strain level identification based on MLST (Multi-Locus Sequence Typing)

Global functions | |
---|---|

buildProfiles | Source code |

calcMLSTScore | Source code |

createCustomRASTProfile | Source code |

createProfile | Source code |

createQuery | Source code |

db.buildCustomDB | Source code |

download.fasta | Source code |

extractOrthologs | Source code |

extractProduct | Source code |

extractRPs.NCBI | Source code |

extractRPs.RAST | Source code |

extractrRNA.RAST | Source code |

filter.j | Source code Source code |

getAssemblySummary | Source code |

getCDSFasta | Source code |

getCounts | Source code |

getGFF | Source code |

getGenomicFasta | Source code |

getRefSeqFasta | Source code |

getRefSeqRNA | Source code |

mlstDB.build | Source code |

mlstDB.extract | Source code |

mlstDB.importGFF | Source code |

mlstDB.resetIDs | Source code |

mlstDB.subset | Source code |

mlstDB.subsetASM | Source code |

mlstverse | Source code |

obtainConsensus | Source code |

readSAM | Source code |

tmp.func2 | Source code |

tmp.func3 | Source code |

updateGID | Source code |

updateGIDs | Source code Source code |

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