# THIS IS ONLY COMPATIBLE WITH shasta 0.8.0.
# IT CANNOT BE USED WITH MORE RECENT RELEASES.

# EXPERIMENTAL configuration file that uses assembly mode 2
# to create a phased diploid assembly.

# Tested with Guppy 5.0.7 Ultra-Long (ULT) reads at coverage around 60x. 



[Reads]
minReadLength = 35000
noCache = True

[Kmers]
k = 14

[MinHash]
minBucketSize = 10
maxBucketSize = 60
minFrequency = 5

[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
minAlignedMarkerCount = 400
minAlignedFraction = 0.6
maxDrift = 20
maxSkip = 50
maxTrim = 50
sameChannelReadAlignment.suppressDeltaThreshold = 30

[ReadGraph]
creationMethod = 0
maxAlignmentCount = 12 
strandSeparationMethod = 2

[MarkerGraph]
minCoverage = 8
minCoveragePerStrand = 1
minEdgeCoverage = 8
minEdgeCoveragePerStrand = 1

[Assembly]
mode = 2
consensusCaller = Bayesian:guppy-5.0.7-a
phasing.minReadCount = 2



