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annotate 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
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2 # GUPPY VERSION OLDER THAN 3.6.0.
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4 # This file contains Shasta options which attempt to partially automate
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5 # parameter selection. It is based on an earlier config, which, as of Jun 2020,
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6 # was known to work with Oxford Nanopore reads under the following circumstances:
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8 # - Human genome assembly.
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9 # - Coverage between 40x and 80x. If you have more coverage than that,
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10 # you can use option "--Reads.minReadLength" to adjust coverage as desired.
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11 # - Reads from Guppy 3.6.0 base caller. If you have reads
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12 # from an older version of Guppy, use configuration file
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13 # Nanopore-UL-Dec2019.conf instead.
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15 # The automation provided by this config is particularly applicable to
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16 # low coverage or non-human samples. It also matches or exceeds continuity
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17 # in human samples, relative to the appropriately chosen 3.6.0 or 3.6.0-UL conf.
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18 # Automation can be activated with parameters designed for earlier basecallers,
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19 # if needed, but updating to guppy 3.6.0 or higher will greatly improve assembly
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20 # quality and is therefore strongly recommended.
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22 # In most cases, for best performance on a large assembly
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23 # you will usually also want to use the following options, which
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24 # cannot be specified in a configuration file:
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25 # --memoryMode filesystem
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26 # --memoryBacking 2M
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27 # Using these options requires root access.
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29 # For detailed information on all available options see here:
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30 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
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32 # For information on running a small assembly for which
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33 # performance is not essential see here:
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34 # https://chanzuckerberg.github.io/shasta/QuickStart.html
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36 # For more information on running an assembly see here:
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37 # https://chanzuckerberg.github.io/shasta/Running.html
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39 # For information on optimizing assembly performance see here:
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40 # https://chanzuckerberg.github.io/shasta/Performance.html
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44 [Reads]
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45 # If you have extra coverage, use this option to adjust coverage.
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46 minReadLength = 50000
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47 noCache = True
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49 [Kmers]
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50 # Due to the higher accuracy of Guppy 3.6.0 we use longer
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51 # markers than usual.
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52 k = 14
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54 [MinHash]
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55 minBucketSize = 10
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56 maxBucketSize = 30
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57 minFrequency = 5
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59 [Align]
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60 alignMethod = 3
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61 downsamplingFactor = 0.05
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62 matchScore = 6
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63 sameChannelReadAlignment.suppressDeltaThreshold = 30
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64
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65 # The following Align parameters are set to very permissive values to allow the majority of alignments
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66 # to be assessed during the initial stage of automatic alignment parameter selection
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67 maxSkip = 100
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68 maxDrift = 100
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69 maxTrim = 100
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70 minAlignedMarkerCount = 10
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71 minAlignedFraction = 0.1
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73 [ReadGraph]
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74 # This method uses the observed distribution of alignment stats to choose a cutoff for
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75 # maxSkip, maxDrift, maxTrim, minAlignedMarkerCount, and minAlignedFraction
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76 creationMethod = 2
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78 [MarkerGraph]
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79 simplifyMaxLength = 10,100,1000,10000,100000
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80 crossEdgeCoverageThreshold = 3
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81
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82 # Automatically determine this using PeakFinder
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83 minCoverage = 0
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84
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85 [Assembly]
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86 consensusCaller = Bayesian:guppy-3.6.0-a
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87 detangleMethod = 2
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89