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comparison configs/Nanopore-Sep2020.conf @ 0:60573349e9ae draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
author iuc
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 which attempt to partially automate
5 # parameter selection. It is based on an earlier config, which, as of Jun 2020,
6 # was known to work with Oxford Nanopore reads 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-Dec2019.conf instead.
14
15 # The automation provided by this config is particularly applicable to
16 # low coverage or non-human samples. It also matches or exceeds continuity
17 # in human samples, relative to the appropriately chosen 3.6.0 or 3.6.0-UL conf.
18 # Automation can also be activated with parameters designed for earlier basecallers,
19 # if needed, but updating to guppy 3.6.0 or higher will greatly improve assembly
20 # quality and is therefore strongly recommended.
21
22 # To use this configuration file, specify Shasta option
23 # "--config AbsolutePathToThisFile".
24 # If you specify any conflicting values on the command line,
25 # the values specified on the command line take precedence.
26
27 # In most cases, for best performance on a large assembly
28 # you will usually also want to use the following options, which
29 # cannot be specified in a configuration file:
30 # --memoryMode filesystem
31 # --memoryBacking 2M
32 # Using these options requires root access.
33
34 # For detailed information on all available options see here:
35 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
36
37 # For information on running a small assembly for which
38 # performance is not essential see here:
39 # https://chanzuckerberg.github.io/shasta/QuickStart.html
40
41 # For more information on running an assembly see here:
42 # https://chanzuckerberg.github.io/shasta/Running.html
43
44 # For information on optimizing assembly performance see here:
45 # https://chanzuckerberg.github.io/shasta/Performance.html
46
47
48
49 [Reads]
50 # If you have extra coverage, use this option to adjust coverage.
51 minReadLength = 10000
52 noCache = True
53
54 [Kmers]
55 # Due to the higher accuracy of Guppy 3.6.0 we use longer
56 # markers than usual.
57 k = 14
58
59 [MinHash]
60 minBucketSize = 5
61 maxBucketSize = 30
62 minFrequency = 5
63
64 [Align]
65 alignMethod = 3
66 downsamplingFactor = 0.05
67 matchScore = 6
68 sameChannelReadAlignment.suppressDeltaThreshold = 30
69
70 # The following Align parameters are set to very permissive values to allow the majority of alignments
71 # to be assessed during the initial stage of automatic alignment parameter selection
72 maxSkip = 100
73 maxDrift = 100
74 maxTrim = 100
75 minAlignedMarkerCount = 10
76 minAlignedFraction = 0.1
77
78 [ReadGraph]
79 # This method uses the observed distribution of alignment stats to choose a cutoff for
80 # maxSkip, maxDrift, maxTrim, minAlignedMarkerCount, and minAlignedFraction
81 creationMethod = 2
82
83 [MarkerGraph]
84 simplifyMaxLength = 10,100,1000,10000,100000
85 crossEdgeCoverageThreshold = 3
86
87 # Automatically determine this using PeakFinder
88 minCoverage = 0
89
90 [Assembly]
91 consensusCaller = Bayesian:guppy-3.6.0-a
92 detangleMethod = 2
93
94