# Shasta assembly configuration for ONT r10.4.1_e8.2-400bps_sup raw reads,
# without error correction, as announced by Oxford Nanopore in May 2024:
# see https://labs.epi2me.io/lc2024_t2t/

[Reads]
representation = 0
minReadLength = 10000
noCache = True
palindromicReads.deltaThreshold = 300

[Kmers]
k = 30
probability = 0.05

[MinHash]
m = 10
minHashIterationCount = 50
minBucketSize = 0
maxBucketSize = 0
minFrequency = 70

[Align]
alignMethod = 6
sameChannelReadAlignment.suppressDeltaThreshold = 30
minAlignedMarkerCount = 500
minAlignedFraction = 0.83
maxSkip = 10
maxDrift = 14
maxTrim = 10
align6.maxInBandCount = 1000000
align6.maxGlobalFrequencyMultiplier = 0.6
align6.minLowFrequencyCount = 6

[ReadGraph]
maxAlignmentCount = 20
strandSeparationMethod = 2
preferAlignedFraction = True

[Assembly]
mode = 3
mode3.primaryGraph.maxLoss = 0.5
mode3.assemblyGraph.phaseErrorThreshold = 0.2
mode3.assemblyGraph.minLogP = 10


