# This configuration file is EXPERIMENTAL and should only
# be used under the following conditions:
# - Nanopore reads created by Guppy 3.6.0 or newer.
# - Ultra-Long (UL) reads with typical N50 80Kb or more.
# - High coverage 80X.
# Iterative assembly results in some separation of haplotypes
# and does better at resolving segmental duplications.

[Reads]
minReadLength = 30000 
noCache = True

[Kmers]
k = 10 

[MinHash]
minBucketSize = 10 
maxBucketSize = 40 
minFrequency = 5 

[Align]
alignMethod = 3 
matchScore = 6
gapScore = -3 
downsamplingFactor = 0.05 
maxSkip = 100
maxDrift = 100
maxTrim = 100
minAlignedMarkerCount = 10
minAlignedFraction = 0.1
sameChannelReadAlignment.suppressDeltaThreshold = 30 

[ReadGraph]
maxAlignmentCount = 12
creationMethod = 2

[MarkerGraph]
minCoveragePerStrand = 3
simplifyMaxLength = 10,100
crossEdgeCoverageThreshold = 3 

[Assembly]
detangleMethod = 2 
consensusCaller = Bayesian:guppy-3.6.0-a
iterative = True

