diff configs/Nanopore-Sep2020.conf @ 0:60573349e9ae draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/configs/Nanopore-Sep2020.conf	Wed Nov 11 21:54:51 2020 +0000
@@ -0,0 +1,94 @@
+# DO NOT USE THIS FILE IF YOU HAVE READS CREATED BY A
+# GUPPY VERSION OLDER THAN 3.6.0.
+
+# This file contains Shasta options which attempt to partially automate
+# parameter selection. It is based on an earlier config, which, as of Jun 2020,
+# was 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 3.6.0 base caller. If you have reads
+#   from an older version of Guppy, use configuration file
+#   Nanopore-Dec2019.conf instead.
+
+# The automation provided by this config is particularly applicable to
+# low coverage or non-human samples. It also matches or exceeds continuity
+# in human samples, relative to the appropriately chosen 3.6.0 or 3.6.0-UL conf.
+# Automation can also be activated with parameters designed for earlier basecallers,
+# if needed, but updating to guppy 3.6.0 or higher will greatly improve assembly
+# quality and is therefore strongly recommended.
+
+# 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 = 10000
+noCache = True
+
+[Kmers]
+# Due to the higher accuracy of Guppy 3.6.0 we use longer
+# markers than usual.
+k = 14
+
+[MinHash]
+minBucketSize = 5
+maxBucketSize = 30
+minFrequency = 5
+
+[Align]
+alignMethod = 3
+downsamplingFactor = 0.05
+matchScore = 6
+sameChannelReadAlignment.suppressDeltaThreshold = 30
+
+# The following Align parameters are set to very permissive values to allow the majority of alignments
+# to be assessed during the initial stage of automatic alignment parameter selection
+maxSkip = 100
+maxDrift = 100
+maxTrim = 100
+minAlignedMarkerCount = 10
+minAlignedFraction = 0.1
+
+[ReadGraph]
+# This method uses the observed distribution of alignment stats to choose a cutoff for
+# maxSkip, maxDrift, maxTrim, minAlignedMarkerCount, and minAlignedFraction
+creationMethod = 2
+
+[MarkerGraph]
+simplifyMaxLength = 10,100,1000,10000,100000
+crossEdgeCoverageThreshold = 3
+
+# Automatically determine this using PeakFinder
+minCoverage = 0
+
+[Assembly]
+consensusCaller = Bayesian:guppy-3.6.0-a
+detangleMethod = 2
+
+