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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805
author iuc
date Thu, 13 Feb 2025 09:20:08 +0000
parents 7a586a157d37
children
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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1 VARVAMP log
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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3 MODE = tiled
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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5 WARNING: your amplicon lengths might be to small. Consider increasing
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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6 WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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8 ARG SETTINGS
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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10 THRESHOLD = 0.6
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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11 PRIMER_ALLOWED_N_AMB = 2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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12 AMPLICON_OPT_LENGTH = 150
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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13 AMPLICON_MAX_LENGTH = 300
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209d074eb024 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805
iuc
parents: 0
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14 MIN_OVERLAP = 76
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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16 CONFIG SETTINGS
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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18 PRIMER_TMP = (56, 63, 60)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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19 PRIMER_GC_RANGE = (35, 65, 50)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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20 PRIMER_SIZES = (18, 24, 21)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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21 PRIMER_HAIRPIN = 47
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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22 PRIMER_MAX_POLYX = 4
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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23 PRIMER_MAX_DINUC_REPEATS = 4
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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24 PRIMER_GC_END = (1, 3)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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25 PRIMER_MAX_DIMER_TMP = 47
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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26 PRIMER_MIN_3_WITHOUT_AMB = 3
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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27 PCR_MV_CONC = 100
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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28 PCR_DV_CONC = 2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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29 PCR_DNTP_CONC = 0.8
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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30 PCR_DNA_CONC = 15
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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31 PRIMER_TM_PENALTY = 2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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32 PRIMER_GC_PENALTY = 0.2
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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33 PRIMER_SIZE_PENALTY = 0.5
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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34 PRIMER_MAX_BASE_PENALTY = 10
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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35 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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36 PRIMER_PERMUTATION_PENALTY = 0.1
7a586a157d37 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d
iuc
parents:
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