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comparison test-data/test2.log @ 0:462e62be07e1 draft

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author iuc
date Sat, 27 Jan 2024 12:34:39 +0000
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-1:000000000000 0:462e62be07e1
1 VARVAMP log
2
3 MODE = tiled
4
5 WARNING: your amplicon lengths might be to small. Consider increasing
6 WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.
7
8 ARG SETTINGS
9
10 THRESHOLD = 0.6
11 PRIMER_ALLOWED_N_AMB = 2
12 AMPLICON_OPT_LENGTH = 150
13 AMPLICON_MAX_LENGTH = 300
14 MIN_OVERLAP = 100
15
16 CONFIG SETTINGS
17
18 PRIMER_TMP = (56, 63, 60)
19 PRIMER_GC_RANGE = (35, 65, 50)
20 PRIMER_SIZES = (18, 24, 21)
21 PRIMER_HAIRPIN = 47
22 PRIMER_MAX_POLYX = 4
23 PRIMER_MAX_DINUC_REPEATS = 4
24 PRIMER_GC_END = (1, 3)
25 PRIMER_MAX_DIMER_TMP = 47
26 PRIMER_MIN_3_WITHOUT_AMB = 3
27 PCR_MV_CONC = 100
28 PCR_DV_CONC = 2
29 PCR_DNTP_CONC = 0.8
30 PCR_DNA_CONC = 15
31 PRIMER_TM_PENALTY = 2
32 PRIMER_GC_PENALTY = 0.2
33 PRIMER_SIZE_PENALTY = 0.5
34 PRIMER_MAX_BASE_PENALTY = 10
35 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
36 PRIMER_PERMUTATION_PENALTY = 0.1
37