diff configs/Nanopore-Dec2019.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-Dec2019.conf	Wed Nov 11 21:54:51 2020 +0000
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+# This file contains Shasta options that, as of December 2019,
+# are known to work with 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 3.0.5 base caller. Also known to work with
+#   reads from other Guppy releases 3.0.x and 3.1.x.
+
+# To use this configuration file, specify Shasta option "--config PathToThisFile". 
+# 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 require 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 = 10000
+
+[MinHash]
+minBucketSize = 5
+maxBucketSize = 30
+minFrequency = 5
+
+[Align]
+minAlignedFraction = 0.4
+
+[Assembly]
+consensusCaller = Bayesian:guppy-3.0.5-a
+