# This was tested on the  "HG002 Data Freeze (v1.0) 
# Recommended downsampled data mix", a 34x HiFi dataset
# for HG002. See here for more information:
# https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0#hg002-data-freeze-v10-recommended-downsampled-data-mix
# It assembled 3078 Mb of sequence with an N50 of 35 Mb.
# The quality of assembled sequence was estimated
# at Q = 46 dB via k-mer based methods. It is limited
# by the fact that this creates a haploid assembly
# in which one of the alleles of each heterozygous locus
# is removed.



[Reads]
minReadLength = 8000
noCache = True

[Kmers]
k = 14

[MinHash]
hashFraction = 0.05
minHashIterationCount = 100
minFrequency = 3
minBucketSize = 10
maxBucketSize = 60

[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
minAlignedFraction = 0.97
minAlignedMarkerCount = 200
maxSkip = 6
maxDrift = 4
maxTrim = 2

[ReadGraph]
maxAlignmentCount = 30
maxChimericReadDistance = 2

[MarkerGraph]
minCoverage = 6
simplifyMaxLength = 10,100,1000,10000,100000
crossEdgeCoverageThreshold = 3

[Assembly]
consensusCaller = Modal
detangleMethod = 2


