Configuration File Template

#Experiment 
Experiment.name = "AptaTRACE"
Experiment.description = "A descrption of the experiment"
Experiment.projectPath = /path/to/the/project/directory

Experiment.primer5 = GGGAGGACGATGCGG

# OPTIONAL, if not specified, we need Experiment.randomizedRegionSize
Experiment.primer3 = CAGACGACTCGCCCGA
# Experiment.randomizedRegionSize = 40

### Selection Cycle Information ###
SelectionCycle.name = Round0
SelectionCycle.round = 0
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round1
SelectionCycle.round = 1
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round2
SelectionCycle.round = 2
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round3
SelectionCycle.round = 3
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round4
SelectionCycle.round = 4
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round5
SelectionCycle.round = 5
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round6
SelectionCycle.round = 6
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round7
SelectionCycle.round = 7
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round8
SelectionCycle.round = 8
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round9
SelectionCycle.round = 9
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

SelectionCycle.name = Round10
SelectionCycle.round = 10
SelectionCycle.isControlSelection = False
SelectionCycle.isCounterSelection = False

#Default is false
AptaplexParser.isPerFile = True

#One or more input files. If AptaplexParser.isPerFile is True, 
#an equal number of files as there are selection cycles must be specified
#and in the same order
AptaplexParser.forwardFiles = /path/to/round_0.fastq
AptaplexParser.forwardFiles = /path/to/round_1.fastq
AptaplexParser.forwardFiles = /path/to/round_2.fastq
AptaplexParser.forwardFiles = /path/to/round_3.fastq
AptaplexParser.forwardFiles = /path/to/round_4.fastq
AptaplexParser.forwardFiles = /path/to/round_5.fastq
AptaplexParser.forwardFiles = /path/to/round_6.fastq
AptaplexParser.forwardFiles = /path/to/round_7.fastq
AptaplexParser.forwardFiles = /path/to/round_8.fastq
AptaplexParser.forwardFiles = /path/to/round_9.fastq
AptaplexParser.forwardFiles = /path/to/round_10.fastq

#Default is fastq
AptaplexParser.reader = FastqReader


### APTACLUSTER OPTIONS ###
# Length of the randomized region in the aptamers
Aptacluster.RandomizedRegionSize = 40

# Number of indices to sample
Aptacluster.LSHDimension = 30

# The number of LSH iterations to be performed
Aptacluster.LSHIterations = 5 

# The kmer size used for the distance calculations
Aptacluster.KmerSize = 3


### APTASIM OPTIONS ###
# Fastq file containing training sequences
# Aptasim.HmmFile = /path/to/training/data.fastq.gz 

# Degree of the Markov model
Aptasim.HmmDegree = 2 

# Length of the randomized region in the aptamers
Aptasim.RandomizedRegionSize = 40

# Number of (unique) sequences in the initial pool
Aptasim.NumberOfSequences = 500000 

# Number of high affinity sequences in the initial pool
Aptasim.NumberOfSeeds = 100 

#The minimal affinity for seed sequences (INT range: 0-100)
Aptasim.MinSeedAffinity = 80

# Maximal count of remaining sequences
Aptasim.MaxSequenceCount = 10

# The maximal sequence affinity for non-seeds (INT range: 0-100)
Aptasim.MaxSequenceAffinity = 25

# If no training data is specified, create pool based on this distribution (order A,C,G,T)
Aptasim.NucleotideDistribution = 0.25, 0.25, 0.25, 0.25

# The percentage of sequences that remain after selection (DOUBLE range: 0-1)
Aptasim.SelectionPercentage = 0.20

# Mutation rates for individual nucleotides (order A,C,G,T)
Aptasim.BaseMutationRates = 0.25, 0.25, 0.25, 0.25

# Mutation probability during PCR (DOUBLE range: 0-1)
Aptasim.MutationProbability = 0.05

# PCR amplification efficiency (DOUBLE range: 0-1)
Aptasim.AmplificationEfficiency = 0.995


### APTATRACE OTIONS ###
Aptatrace.KmerLength=6

Aptatrace.FilterClusters=True

Aptatrace.OutputClusters=True

Aptatrace.Alpha=10


### EXPORT OPTIONS ###
Export.Cycles = Round0, Round5, Round8

### PERFORMANCE OPTIONS ###
Performance.maxNumberOfCores = 30