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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86
author iuc
date Sat, 15 Jun 2024 15:43:28 +0000
parents 462e62be07e1
children
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VARVAMP log 

MODE = single


ARG SETTINGS

THRESHOLD = 0.8
PRIMER_ALLOWED_N_AMB = 3
AMPLICON_OPT_LENGTH = 300
AMPLICON_MAX_LENGTH = 400
REPORT_N_AMPLICONS = 5

CONFIG SETTINGS

PRIMER_TMP = (56, 63, 60)
PRIMER_GC_RANGE = (20, 80, 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 = 100.0
PCR_DV_CONC = 2.0
PCR_DNTP_CONC = 0.8
PCR_DNA_CONC = 15.0
PRIMER_TM_PENALTY = 2.0
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