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comparison configs/Nanopore-UL-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-UL-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 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 # In most cases, for best performance on a large assembly
23 # you will usually also want to use the following options, which
24 # cannot be specified in a configuration file:
25 # --memoryMode filesystem
26 # --memoryBacking 2M
27 # Using these options requires root access.
28
29 # For detailed information on all available options see here:
30 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
31
32 # For information on running a small assembly for which
33 # performance is not essential see here:
34 # https://chanzuckerberg.github.io/shasta/QuickStart.html
35
36 # For more information on running an assembly see here:
37 # https://chanzuckerberg.github.io/shasta/Running.html
38
39 # For information on optimizing assembly performance see here:
40 # https://chanzuckerberg.github.io/shasta/Performance.html
41
42
43
44 [Reads]
45 # If you have extra coverage, use this option to adjust coverage.
46 minReadLength = 50000
47 noCache = True
48
49 [Kmers]
50 # Due to the higher accuracy of Guppy 3.6.0 we use longer
51 # markers than usual.
52 k = 14
53
54 [MinHash]
55 minBucketSize = 10
56 maxBucketSize = 30
57 minFrequency = 5
58
59 [Align]
60 alignMethod = 3
61 downsamplingFactor = 0.05
62 matchScore = 6
63 sameChannelReadAlignment.suppressDeltaThreshold = 30
64
65 # The following Align parameters are set to very permissive values to allow the majority of alignments
66 # to be assessed during the initial stage of automatic alignment parameter selection
67 maxSkip = 100
68 maxDrift = 100
69 maxTrim = 100
70 minAlignedMarkerCount = 10
71 minAlignedFraction = 0.1
72
73 [ReadGraph]
74 # This method uses the observed distribution of alignment stats to choose a cutoff for
75 # maxSkip, maxDrift, maxTrim, minAlignedMarkerCount, and minAlignedFraction
76 creationMethod = 2
77
78 [MarkerGraph]
79 simplifyMaxLength = 10,100,1000,10000,100000
80 crossEdgeCoverageThreshold = 3
81
82 # Automatically determine this using PeakFinder
83 minCoverage = 0
84
85 [Assembly]
86 consensusCaller = Bayesian:guppy-3.6.0-a
87 detangleMethod = 2
88
89