diff configs/Nanopore-UL-Jun2020.conf @ 0:60573349e9ae draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"

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+++ b/configs/Nanopore-UL-Jun2020.conf	Wed Nov 11 21:54:51 2020 +0000
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+# DO NOT USE THIS FILE IF YOU HAVE READS CREATED BY A
+# GUPPY VERSION OLDER THAN 3.6.0.
+
+# This file contains Shasta options that, as of June 2020,
+# are known to work with Ultra-Long (UL) Oxford Nanopore reads 
+# under the following circumstances:
+
+# - Human genome assembly.
+# - Coverage between 40x and 80x. If you have more coverage than that,
+#   you can use option "--Reads.minReadLength" to adjust coverage as desired.
+# - Reads from Guppy 3.6.0 base caller. If you have reads
+#   from an older version of Guppy, use configuration file
+#   Nanopore-UL-Dec2019.conf instead.
+
+# To use this configuration file, specify Shasta option 
+# "--config AbsolutePathToThisFile". 
+# If you specify any conflicting values on the command line,
+# the values specified on the command line take precedence.
+
+# In most cases, for best performance on a large assembly 
+# you will usually also want to use the following options, which 
+# cannot be specified in a configuration file:
+# --memoryMode filesystem
+# --memoryBacking 2M
+# Using these options requires root access.
+
+# For detailed information on all available options see here:
+# https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
+
+# For information on running a small assembly for which 
+# performance is not essential see here:
+# https://chanzuckerberg.github.io/shasta/QuickStart.html
+
+# For more information on running an assembly see here:
+# https://chanzuckerberg.github.io/shasta/Running.html
+
+# For information on optimizing assembly performance see here:
+# https://chanzuckerberg.github.io/shasta/Performance.html
+
+
+
+[Reads]
+# If you have extra coverage, use this option to adjust coverage.
+minReadLength = 50000
+noCache = True
+
+[Kmers]
+# Due to the higher accuracy of Guppy 3.6.0 we use longer
+# markers than usual.
+k = 14
+
+[MinHash]
+minBucketSize = 10
+maxBucketSize = 30
+minFrequency = 5
+
+[Align]
+alignMethod = 3
+downsamplingFactor = 0.05
+matchScore = 6
+minAlignedFraction = 0.55
+minAlignedMarkerCount = 600
+sameChannelReadAlignment.suppressDeltaThreshold = 30
+
+[ReadGraph]
+maxAlignmentCount = 12
+
+
+[MarkerGraph]
+simplifyMaxLength = 10,100,1000,10000,100000
+refineThreshold = 6
+crossEdgeCoverageThreshold = 3
+
+[Assembly]
+consensusCaller = Bayesian:guppy-3.6.0-a
+detangleMethod = 1
+
+