# Shasta assembly configuration specialized for phased diploid 
# human assemblies at low coverage using
# a single flowcell of nanopore reads.
# Because of low coverage, it assembles relatively smalll diploid bubbles.
# 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.
# - Phased diploid assembly.



[Reads]
noCache = True

[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]
strandSeparationMethod = 2
maxAlignmentCount = 12

[MarkerGraph]
minCoverage = 6
minCoveragePerStrand = 1
minEdgeCoverage = 6
minEdgeCoveragePerStrand = 1

[Assembly]
mode = 2
consensusCaller = Bayesian:guppy-5.0.7-b
pruneLength = 100
mode2.bubbleRemoval.minConcordantReadCount = 2





