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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1626c59de1e3aa8a9ccb8674b38a4654a03ab44b
author iuc
date Fri, 05 Apr 2024 20:15:39 +0000
parents 462e62be07e1
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VARVAMP log 

MODE = tiled

WARNING: your amplicon lengths might be to small. Consider increasing
WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.

ARG SETTINGS

THRESHOLD = 0.6
PRIMER_ALLOWED_N_AMB = 2
AMPLICON_OPT_LENGTH = 150
AMPLICON_MAX_LENGTH = 300
MIN_OVERLAP = 100

CONFIG SETTINGS

PRIMER_TMP = (56, 63, 60)
PRIMER_GC_RANGE = (35, 65, 50)
PRIMER_SIZES = (18, 24, 21)
PRIMER_HAIRPIN = 47
PRIMER_MAX_POLYX = 4
PRIMER_MAX_DINUC_REPEATS = 4
PRIMER_GC_END = (1, 3)
PRIMER_MAX_DIMER_TMP = 47
PRIMER_MIN_3_WITHOUT_AMB = 3
PCR_MV_CONC = 100
PCR_DV_CONC = 2
PCR_DNTP_CONC = 0.8
PCR_DNA_CONC = 15
PRIMER_TM_PENALTY = 2
PRIMER_GC_PENALTY = 0.2
PRIMER_SIZE_PENALTY = 0.5
PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1