Mercurial > repos > iuc > shasta
comparison configs/Nanopore-UL-Jun2020.conf @ 0:60573349e9ae draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
author | iuc |
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date | Wed, 11 Nov 2020 21:54:51 +0000 |
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1 # DO NOT USE THIS FILE IF YOU HAVE READS CREATED BY A | |
2 # GUPPY VERSION OLDER THAN 3.6.0. | |
3 | |
4 # This file contains Shasta options that, as of June 2020, | |
5 # are known to work with Ultra-Long (UL) Oxford Nanopore reads | |
6 # under the following circumstances: | |
7 | |
8 # - Human genome assembly. | |
9 # - Coverage between 40x and 80x. If you have more coverage than that, | |
10 # you can use option "--Reads.minReadLength" to adjust coverage as desired. | |
11 # - Reads from Guppy 3.6.0 base caller. If you have reads | |
12 # from an older version of Guppy, use configuration file | |
13 # Nanopore-UL-Dec2019.conf instead. | |
14 | |
15 # To use this configuration file, specify Shasta option | |
16 # "--config AbsolutePathToThisFile". | |
17 # If you specify any conflicting values on the command line, | |
18 # the values specified on the command line take precedence. | |
19 | |
20 # In most cases, for best performance on a large assembly | |
21 # you will usually also want to use the following options, which | |
22 # cannot be specified in a configuration file: | |
23 # --memoryMode filesystem | |
24 # --memoryBacking 2M | |
25 # Using these options requires root access. | |
26 | |
27 # For detailed information on all available options see here: | |
28 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html | |
29 | |
30 # For information on running a small assembly for which | |
31 # performance is not essential see here: | |
32 # https://chanzuckerberg.github.io/shasta/QuickStart.html | |
33 | |
34 # For more information on running an assembly see here: | |
35 # https://chanzuckerberg.github.io/shasta/Running.html | |
36 | |
37 # For information on optimizing assembly performance see here: | |
38 # https://chanzuckerberg.github.io/shasta/Performance.html | |
39 | |
40 | |
41 | |
42 [Reads] | |
43 # If you have extra coverage, use this option to adjust coverage. | |
44 minReadLength = 50000 | |
45 noCache = True | |
46 | |
47 [Kmers] | |
48 # Due to the higher accuracy of Guppy 3.6.0 we use longer | |
49 # markers than usual. | |
50 k = 14 | |
51 | |
52 [MinHash] | |
53 minBucketSize = 10 | |
54 maxBucketSize = 30 | |
55 minFrequency = 5 | |
56 | |
57 [Align] | |
58 alignMethod = 3 | |
59 downsamplingFactor = 0.05 | |
60 matchScore = 6 | |
61 minAlignedFraction = 0.55 | |
62 minAlignedMarkerCount = 600 | |
63 sameChannelReadAlignment.suppressDeltaThreshold = 30 | |
64 | |
65 [ReadGraph] | |
66 maxAlignmentCount = 12 | |
67 | |
68 | |
69 [MarkerGraph] | |
70 simplifyMaxLength = 10,100,1000,10000,100000 | |
71 refineThreshold = 6 | |
72 crossEdgeCoverageThreshold = 3 | |
73 | |
74 [Assembly] | |
75 consensusCaller = Bayesian:guppy-3.6.0-a | |
76 detangleMethod = 1 | |
77 | |
78 |