# This was used in April 2021 for an assembly of Lolium Perenne
# under the following conditions:

# - Oxford Nanopore reads, basecalled with Guppy 4.0.14.
# - Coverage: 30x.
# - Reads N50: 62 Kb. 

# The assembly was run:

# - Using Shasta at commit 266d4c8e65ff408db2dfd1381bb14648be83dad3.
# - On AWS Graviton2 (ARM) r6g.16xlarge instance type, 512 GB, 64 vCPUs.
# - Using memory options --memoryMode filesystem --memoryBacking 2M.

# Assembly results:

# - Assembled 2.185 Mb of sequence. Estimated genome size 
#   is 2.46 Gb from k-mer analysis, 2.72 Gb from flow cytometry.
# - Assembly N50: 5.5 Mb.
# - Elapsed time for assembly: 95 minutes.

# Many thanks to Dario Copetti (Molecular Plant Breeding, ETH Zurich, Switzerland)
# for providing access to the reads in advance of publication. 

# Also see Shasta issue #200 for some discussion
# https://github.com/paoloshasta/shasta/issues/200



[Reads]
noCache = True

[MinHash]
minBucketSize = 5
maxBucketSize = 30
minHashIterationCount = 50
minFrequency = 5

[Align]
downsamplingFactor = 0.05
sameChannelReadAlignment.suppressDeltaThreshold = 30
maxSkip = 60
maxDrift = 20
maxTrim = 60
minAlignedMarkerCount = 200
minAlignedFraction = 0.3

[MarkerGraph]
simplifyMaxLength = 10,100,1000,10000,100000
crossEdgeCoverageThreshold = 3
minCoverage = 0

[Assembly]
consensusCaller = Bayesian:guppy-3.6.0-a
detangleMethod = 2


