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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
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General Sequence of Events #3

Closed kwade4 closed 3 years ago

kwade4 commented 3 years ago

  1. Input validation (sequence lengths, properly formatted headers)

  2. Unmask / Mask (masked sequences omitted in initial analysis step)

  3. Initial analysis (command22_click)

    • Run BOOTSCAN, GENECOV, MaxChi, Chimaera, Siscan, 3SEQ, RDP
    • Identify number of unique recombination of events
    • Output: PDist, P-vals, #Hits

  4. Secondary analysis

    • Handle multiple identifications of same recombination event (if any) by selecting sequence with strongest signal, erasing a portion of the sequence, and reanalyzing, until no signals are detected.
    • Include masked sequences in analyses
    • Output: BPNum