# Shasta assembly configuration specialized for human assemblies
# at low coverage using a single flowcell of nanopore reads.
# It is meant to be used under the following conditions:
#
# - Human genome.
# - Nanopore reads, single flowcell (100-120 Gb of coverage or around 35x).
# - Guppy 5.0.7 base caller or newer, with "super" accuracy.
# - Read N50 around 30 Kb.
# - Haploid assembly.



[Reads]
minReadLength = 10000
noCache = True

[Kmers]
k = 14

[MinHash]
minBucketSize = 5
maxBucketSize = 30
minHashIterationCount = 100
minFrequency = 5

[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
sameChannelReadAlignment.suppressDeltaThreshold = 30
maxSkip = 30
maxDrift = 15
maxTrim = 30
minAlignedMarkerCount = 200
minAlignedFraction = 0.6

[ReadGraph]
creationMethod = 0
maxAlignmentCount = 12

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

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

[Assembly]
consensusCaller = Bayesian:guppy-5.0.7-b
detangleMethod = 2

