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view test-data/test2.log @ 1:80e18c0836e5 draft
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1626c59de1e3aa8a9ccb8674b38a4654a03ab44b
author | iuc |
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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