# This Shasta assembly configuration was tested under the following conditions:
#  - ONT R10 chemistry, fast mode, chimera rate around 2%.
#  - Guppy 6 basecaller with "super" accuracy.
#  - Human genome at low coverage (one flowcell, coverage around 35x).
#  - Haploid assembly.
# Under these conditions it produced a haploid assembly with N50 around 20 Mb
# and with base level accuracy limited mostly by heterozygosity 
# of the human genome.  
# This configuration might also be usable for other genomes and at higher coverage,
# but that was not tested.

[Reads]
representation = 0
minReadLength = 10000
noCache = True

[Kmers]
k = 14

[MinHash]
minHashIterationCount = 100
minBucketSize = 10
maxBucketSize = 40
minFrequency = 5

[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
sameChannelReadAlignment.suppressDeltaThreshold = 30
minAlignedMarkerCount = 1000
minAlignedFraction = 0.85
maxSkip = 20
maxDrift = 10
maxTrim = 20

[ReadGraph]
creationMethod = 0
maxAlignmentCount = 15

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

# Adaptive estimation of coverage threshold to generate marker graph vertices.
minCoverage = 0

[Assembly]
consensusCaller = Modal
detangleMethod = 2