Mercurial > repos > iuc > varvamp
diff test-data/test2.log @ 0:462e62be07e1 draft
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author | iuc |
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date | Sat, 27 Jan 2024 12:34:39 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.log Sat Jan 27 12:34:39 2024 +0000 @@ -0,0 +1,37 @@ +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 +