[Reads]
minReadLength = 10000
palindromicReads.maxSkip = 100
palindromicReads.maxMarkerFrequency = 10
palindromicReads.alignedFractionThreshold = 0.1
palindromicReads.nearDiagonalFractionThreshold = 0.1
palindromicReads.deltaThreshold = 100

[Kmers]
k = 10
probability = 0.1

[MinHash]
m = 4
hashFraction = 0.01
minHashIterationCount = 10
maxBucketSize = 10
minFrequency = 2

[Align]
maxSkip = 30
maxMarkerFrequency = 10
minAlignedMarkerCount = 100
maxTrim = 30

[ReadGraph]
maxAlignmentCount = 6
minComponentSize = 100
maxChimericReadDistance = 2

[MarkerGraph]
minCoverage = 10
maxCoverage = 100
lowCoverageThreshold = 0
highCoverageThreshold = 256
maxDistance = 30
edgeMarkerSkipThreshold = 100
pruneIterationCount = 6
simplifyMaxLength = 10,100,1000

[Assembly]
markerGraphEdgeLengthThresholdForConsensus = 1000
consensusCaller = SimpleConsensusCaller
useMarginPhase = False
storeCoverageData = False

