# This file contains Shasta options that, as of December 2019,
# are known to work with PacBio CCS 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.

# 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

[Kmers]
k = 15
probability = 0.02

[MinHash]
m = 12
minBucketSize = 20 
maxBucketSize = 100
minHashIterationCount = 25 
minFrequency = 10

[ReadGraph]
maxAlignmentCount = 20 

[Assembly]
consensusCaller = Modal