
# Configuration file that uses assembly mode 2
# to create a phased diploid assembly using 
# Nanopore Ultra-Long (UL) reads.

# This is known to work at least under the following conditions:
# - Oxford Nanopore Ultra-Long (UL) reads with read N50 50 Kb or more.
# - Guppy 5 base caller with "super" accuracy.
# - Human genome.
# - Coverage 60x to 80x. If you have more coverage, 
#   adjust --Reads.minReadLength or --Reads.desiredCoverage
#   to bring coverage down to this range.
#   For a human genome you can set --Reads.desiredCoverage 200G. 



[Reads]
# Read length cutoff for UL reads, adjust as necessary,
# or use desiredCoverage option to get coverage 
# around 40x to 80x.
minReadLength = 50000
noCache = True



[MinHash]
minBucketSize = 10
maxBucketSize = 50
minFrequency = 5



[Align]
alignMethod = 3
downsamplingFactor = 0.05
matchScore = 6
sameChannelReadAlignment.suppressDeltaThreshold = 30

# Permissive alignment criteria as required for read graph creation method 2.
maxSkip = 100
maxDrift = 100
maxTrim = 100
minAlignedMarkerCount = 10
minAlignedFraction = 0.1



[ReadGraph]

# Automatic adjustment of alignment criteria.
creationMethod = 2

# Strict strand separation is required for Mode 2 (phased) assembly.
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





