config.yaml

# PLEASE ADJUST THE FOLLOWING PARAMETERS -------------------------------------------------------------------------------------------

#Programs/binaries that shall be used
minimap2Bin: "/vol/biotools/bin/minimap2"
merylBin: "../software/Winnowmap/bin/meryl"
WinnowmapBin: "../software/Winnowmap/bin/winnowmap"
#Basename of reference file used for mapping (without path and file suffix)
ref: "t2thumanChrY"

#-----------------------------------------------------------------------------------------------------------------------------------


# DO NOT ADJUST THE FOLLOWING PARAMETERS (unless you know what you are doing) -

globalSeed: 3096671072007954294
kmerBlacklistName: "highAbundKmersMiniK15w10Lrgr100BtStrnds"
eskemapDecent: 0.08758516
eskemapIntercept: -231.1585158515809

simMeasure: ["intersec", "algnWoutOffs"]
nbSimSeqs: 100
simSeqLen: 10000
minimap2DefaultK: 15
minimap2DefaultW: 10
mutationRates: [0, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1]
geneLen: 1000
nbCpys: 3
randSeqLen: 500
nbRandSeqs: 400
pbsimOutFlSufs: ["ref", "fastq", "maf"]
errorPatterns: ["23:31:46", "46:62:92", "92:124:184", "184:248:368", "368:496:736"]
randomSampleSize: 1000
genomes: ["SAL_GB9998AA_AS", "humanChr20", "wheetChr1A-D"] #, "GCF_000001405.40_GRCh38.p14_genomic" 
bwaIdxFileSufs: ["amb", "ann", "bwt", "pac", "sa"]
prog: ["minimap2", "bwamem"]
scoringPatterns: ["c1_u1", "c1_u3", "c9_u1"]
implType: ["Py", "Cpp"]
divergenceRates: [0.01, 0.05]
substitutionIndelRates: [0.5, 1, 2]
copyNumber: 3
templLen: 50000
k: [9, 12, 15] #15 = default of minimap2 and Winnowmap2
PacBioPolymerase: "P6C4"
readCoverage: 2
readLength: 20000
matchScores: [1, 5, 10, 15, 30]
homologyThresholds: [0, -1000, -2000]
benchRepRuns: 10
readLens: [100, 250075, 500050, 750025, 1000000]
refRdRatio: 1.1
t2tChrYlen: 62460029
pbsimLenMin: 100
pbsimLenMax: 1000000
pbsimLenAvg: 9000
pbsimLenStd: 7000
hashRate: 0.3
minimap2HifiK: 19
minimap2HifiW: 19
rlyMppdRdsThrs: [10, 20] 
blastEvalue: 0.01
compTools: ["minimap2", "Winnowmap2"]