# This assembly configuration is for nanopore reads generated using the 
# "Experimental extremely high-accuracy, ultra-long sequencing kit"
# from the ONT December 2023 data release:
# https://labs.epi2me.io/gm24385_ncm23_preview/

# It uses Mode 3 assembly to create a phased assembly.
# It was only tested for a human genome at coverage 40x to 60x,
# but it should work at lower or higher coverage,
# within reasonable limits, because it includes some
# provisions for coverage adaptivity.

[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 = 1000
minAlignedFraction = 0.9
maxSkip = 20
maxDrift = 10
maxTrim = 20

[ReadGraph]
maxAlignmentCount = 20
strandSeparationMethod = 2

[Assembly]
mode = 3


