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annotate configs/PacBio-CCS-Dec2019.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"
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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 PacBio CCS 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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9 # To use this configuration file, specify Shasta option "--config PathToThisFile".
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10 # If you specify any conflicting values on the command line,
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11 # the values specified on the command line take precedence.
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13 # In most cases, for best performance on a large assembly
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14 # you will usually also want to use the following options, which
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15 # cannot be specified in a configuration file:
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16 # --memoryMode filesystem
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17 # --memoryBacking 2M
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18 # Using these options require root access.
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20 # For detailed information on all available options see here:
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21 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
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23 # For information on running a small assembly for which
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24 # performance is not essential see here:
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25 # https://chanzuckerberg.github.io/shasta/QuickStart.html
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27 # For more information on running an assembly see here:
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28 # https://chanzuckerberg.github.io/shasta/Running.html
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30 # For information on optimizing assembly performance see here:
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31 # https://chanzuckerberg.github.io/shasta/Performance.html
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33 [Kmers]
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34 k = 15
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35 probability = 0.02
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37 [MinHash]
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38 m = 12
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39 minBucketSize = 20
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40 maxBucketSize = 100
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41 minHashIterationCount = 25
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42 minFrequency = 10
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44 [ReadGraph]
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45 maxAlignmentCount = 20
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47 [Assembly]
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48 consensusCaller = Modal
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