# This Shasta assembly configuration for phased diploid assembly
# was tested under the following conditions:

#  - ONT R10 chemistry, slow mode, chimera rate around 2%.
#  - Guppy 6 basecaller with "super" accuracy.
#  - Human genome at medium coverage (HG002, two flowcells, coverage around 45x).
#  - Phased diploid assembly.

# Under these conditions, a test run for HG002 produced an assembly 
# consisting of about 2.7 Gb in bubble chains and 0.3 Gb outside bubble chains.
# Of the 2.7 Gb in bubble chains, about 2.2 Gb were assembled diploid and phased. 

# The N50 for bubble chains and the N50 for phased bubbles was about 10 Mb.


# When mapping each branch of a phased bubble against the correct reference haplotype
# for HG002, base level quality was around Q = 50 dB for mismatches,
# and around Q = 40 dB for indels.

# The fraction assembled diploid and phased can be improved with the use of 
# Ultra-Long reads (e. g. 2.7 Gb were assembled diploid and phased with R9, 
# Ultra-Long reads at high coverage). A separate assembly configuration
# for phased diploid assembly using R10 Ultra-Long reads will
# be provided when possible. 

# This configuration might also be usable under different conditions,
# but that was not tested.



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

[Kmers]
k = 14

[MinHash]
minHashIterationCount = 100
minBucketSize = 20
maxBucketSize = 60
minFrequency = 5

[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
sameChannelReadAlignment.suppressDeltaThreshold = 30
minAlignedMarkerCount = 1200
minAlignedFraction = 0.9
maxSkip = 12
maxDrift = 8
maxTrim = 10

[ReadGraph]
creationMethod = 0
strandSeparationMethod = 2
maxAlignmentCount = 15

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


[Assembly]
mode = 2
consensusCaller = Modal
pruneLength = 100
mode2.bubbleRemoval.minConcordantReadCount = 2



