# THIS IS ONLY COMPATIBLE WITH shasta 0.8.0.
# IT CANNOT BE USED WITH MORE RECENT RELEASES.

# EXPERIMENTAL configuration file that uses assembly mode 2
# to create a phased diploid assembly.

# Suitable for Guppy 5.0.7 reads at coverage 40x to 80x. 

# Same as Nanopore-Sep2020.conf, except for the following:
# - Added options to use assembly mode 2.
# - Removed options that are not relevant for assembly mode 2.
# - Bayesian consensus caller for Guppy 5.0.7.



[Reads]
minReadLength = 10000
noCache = True

[Kmers]
k = 14

[MinHash]
minBucketSize = 5
maxBucketSize = 30
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]
creationMethod = 2
strandSeparationMethod = 2

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

[Assembly]
mode = 2
consensusCaller = Bayesian:guppy-5.0.7-a



