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Bioinformatic tool for checking CCHFV molecular detection assays

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cesaregruber/CCHFV-PrimerChecker

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CCHFV-PrimerChecker

Bioinformatic tool to evaluate detection efficacy of existing molecular assays and to propose specific sets of assays to detect as much as possible CCHFV strains from all geographic regions.

Reference: Gruber CEM, Bartolini B, Castilletti C, et al. Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays. Viruses. 2019;11(10):953. Published 2019 Oct 16. doi:10.3390/v11100953

Instructions:

The software is ready-to-use and no need any compilation.

  • If you use CCHFV-PrimerChecker in your PC for the first time:
  1. clone the folders "bins" and "inputfiles" in your local directory;
  2. open a shell (Linux) or a prompt (Windows) in that directory;
  3. digit: "python bins/CCHFVPrimerChecker.py";
  4. search for the file "PrimersMatches_RESULTS.xls" in your local directory: here you can find the result of all the anayzed in the reference work.
  • If you want to compare a new assay with the previously analyzed:

    a) open the Primers_table.csv file in folder "inputfiles";

    b) compile the file adding all the informations of the primers/probes of the new assay;

    c) follow the instructions from 2) to 4).

  • If you want to add a new sequence to the S segment database:

    a) open the CCHFVsequences.fasta file in folder "inputfiles";

    b) add the new sequence to the file;

    c) open the CCHFVsequencesAligned.fasta file in folder "inputfiles";

    d) align the CCHFVsequencesAligned.fasta using your preferred aligner tool;

    e) save the new file as "CCHFVsequencesAligned.fasta";

    f) chek the refence sequence "NC_005302_S_Aligned.fasta" is well aligned with the new "CCHFVsequencesAligned.fasta";

    g) follow the instructions from 2) to 4).

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Bioinformatic tool for checking CCHFV molecular detection assays

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