example.clean.reseq.input

#example input file to clean resequencing reads prior to assembly (9 June 2013)

#input fastq files (make sure left and right match up in the order)
#path to paired end files
files=/PATH/TO/FASTQ/FILES
#files
file1=( sampleA.read1.gz sampleB.read1.gz )
file2=( sampleB.read2.gz sampleB.read2.gz )
#id
id=( sampleA sampleB )

#general parameter
minlen=30	#minimum read length to output in final file

#trimmomatic parameters
adapter=/PATH/TO/ADAPTER/FILE/adapter.fasta
score=-phred33	#-phred33 or -phred64
headCropLen=0
seedMismatches=2
palindromeClipThreshold=30
simpleClipThreshold=12
windowSize=4
windowQuality=20
leadQuality=10
trailQuality=10
path_trimmomatic=/PATH/TO/trimmomatic.jar

#flash parameters
minOverlap=15
maxOverlap=70 #or calc from readlen, frag len, sd [70 is default for 100bp reads, 180bp frag, 18sd]
maxMismatchDensity=0.2

#Quake/Jellyfish parameters
quakeK=19
cov_cut=1
path_quake=/PATH/TO/QUAKE/DIR/

#misc system and log files
threads=6
resourcelog=resource.log

#email for notification
email=name@domain.com