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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"
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1 # This file contains Shasta options that, as of December 2019,
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2 # are known to work with Oxford Nanopore reads under the following
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3 # circumstances:
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5 # - Human genome assembly.
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6 # - Coverage between 40x and 80x. If you have more coverage than that,
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7 # you can use option "--Reads.minReadLength" to adjust coverage as desired.
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8 # - Reads from Guppy 3.0.5 base caller. Also known to work with
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9 # reads from other Guppy releases 3.0.x and 3.1.x.
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11 # To use this configuration file, specify Shasta option "--config PathToThisFile".
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12 # If you specify any conflicting values on the command line,
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13 # the values specified on the command line take precedence.
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15 # In most cases, for best performance on a large assembly
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16 # you will usually also want to use the following options, which
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17 # cannot be specified in a configuration file:
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18 # --memoryMode filesystem
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19 # --memoryBacking 2M
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20 # Using these options require root access.
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22 # For detailed information on all available options see here:
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23 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
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25 # For information on running a small assembly for which
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26 # performance is not essential see here:
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27 # https://chanzuckerberg.github.io/shasta/QuickStart.html
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29 # For more information on running an assembly see here:
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30 # https://chanzuckerberg.github.io/shasta/Running.html
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32 # For information on optimizing assembly performance see here:
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33 # https://chanzuckerberg.github.io/shasta/Performance.html
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37 [Reads]
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38 # If you have extra coverage, use this option to adjust coverage.
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39 minReadLength = 10000
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41 [MinHash]
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42 minBucketSize = 5
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43 maxBucketSize = 30
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44 minFrequency = 5
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46 [Align]
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47 minAlignedFraction = 0.4
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49 [Assembly]
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50 consensusCaller = Bayesian:guppy-3.0.5-a
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