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annotate configs/Nanopore-UL-iterative-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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60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
iuc
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1 # This configuration file is EXPERIMENTAL and should only
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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2 # be used under the following conditions:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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3 # - Nanopore reads created by Guppy 3.6.0 or newer.
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4 # - Ultra-Long (UL) reads with typical N50 80Kb or more.
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5 # - High coverage 80X.
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6 # Iterative assembly results in some separation of haplotypes
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7 # and does better at resolving segmental duplications.
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8
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9 [Reads]
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10 minReadLength = 30000
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11 noCache = True
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13 [Kmers]
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14 k = 10
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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16 [MinHash]
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17 minBucketSize = 10
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18 maxBucketSize = 40
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19 minFrequency = 5
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21 [Align]
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22 alignMethod = 3
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23 matchScore = 6
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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24 gapScore = -3
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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25 downsamplingFactor = 0.05
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26 maxSkip = 100
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27 maxDrift = 100
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28 maxTrim = 100
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29 minAlignedMarkerCount = 10
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30 minAlignedFraction = 0.1
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31 sameChannelReadAlignment.suppressDeltaThreshold = 30
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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33 [ReadGraph]
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34 maxAlignmentCount = 12
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35 creationMethod = 2
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37 [MarkerGraph]
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38 minCoveragePerStrand = 3
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39 simplifyMaxLength = 10,100
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40 crossEdgeCoverageThreshold = 3
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42 [Assembly]
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43 detangleMethod = 2
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44 consensusCaller = Bayesian:guppy-3.6.0-a
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45 iterative = True
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