# 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 = 30
probability = 0.05

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

[Align]
alignMethod = 5
sameChannelReadAlignment.suppressDeltaThreshold = 30
minAlignedMarkerCount = 700
minAlignedFraction = 0.99
maxSkip = 20
maxDrift = 10
maxTrim = 20
align5.driftRateTolerance = 0.05
align5.minBandExtend = 10

[ReadGraph]
maxAlignmentCount = 40
strandSeparationMethod = 2

[Assembly]
mode = 3
mode3.primaryGraph.maxLoss = 0.5

