# Shasta assembly configuration for ONT r10.4.1_e8.2-400bps_sup reads,
# error-corrected with HERRO, 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 = 50
probability = 0.05

[MinHash]
minHashIterationCount = 50
minBucketSize = 0
maxBucketSize = 0
minFrequency = 5

[Align]
alignMethod = 5
sameChannelReadAlignment.suppressDeltaThreshold = 30
minAlignedMarkerCount = 500
minAlignedFraction = 0.98
maxSkip = 50
maxDrift = 50
maxTrim = 50
align5.driftRateTolerance = 0.05
align5.minBandExtend = 10

[ReadGraph]
creationMethod = 4
maxAlignmentCount = 10
strandSeparationMethod = 0
maxChimericReadDistance = 0
epsilon = 1e-4
delta = 5e-4
WThreshold = 1e-8
WThresholdForBreaks = 1e+15

[Assembly]
mode = 3
mode3.primaryGraph.maxLoss = 0.5
mode3.minAnchorCoverage = 0
mode3.maxAnchorCoverage = 0
mode3.maxAnchorCoverageMultiplier = 1.18
mode3.assemblyGraph.pruneLength = 150000

