# 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://paoloshasta.github.io/shasta/CommandLineOptions.html

# For information on running a small assembly for which 
# performance is not essential see here:
# https://paoloshasta.github.io/shasta/QuickStart.html

# For more information on running an assembly see here:
# https://paoloshasta.github.io/shasta/Running.html

# For information on optimizing assembly performance see here:
# https://paoloshasta.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

