#maximal read length
max_rd_len=150
[LIB]
#average insert size
avg_ins=800
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=150
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
q1=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
q2=/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz