# 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 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.

# 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
minAlignedFraction = 0.55
minAlignedMarkerCount = 400
sameChannelReadAlignment.suppressDeltaThreshold = 30

[MarkerGraph]
simplifyMaxLength = 10,100,1000,10000,100000
refineThreshold = 6
crossEdgeCoverageThreshold = 3

[Assembly]
consensusCaller = Bayesian:guppy-3.6.0-a
detangleMethod = 1


