PARAMETERS

GRAPH_KMER_SIZE=auto
USE_LINKING_MATES=1
LIMIT_JUMP_COVERAGE=300
CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.15 ovlMemory=256GB
NUM_THREADS=32
JF_SIZE=4000000000
DO_HOMOPOLYMER_TRIM=0

KMER_COUNT_THRESHOLD = 1
EXTEND_JUMP_READS=0
END

DATA
PE  = pe 300 100    /scratch/c770/c7701100/Dnig_Genome_reads/HI.1859.004.Index_1.Dnig1_replacement_R1.fastq /scratch/c770/c7701100/Dnig_Genome_reads/HI.1859.004.Index_1.Dnig1_replacement_R2.fastq
JUMP= l1 1400 500   /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_19.Pool_Dnig_2kb_R1.fastq /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_19.Pool_Dnig_2kb_R2.fastq
JUMP= l2 4500 700  /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_7.Pool_Dnig_5kb_R1.fastq /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_7.Pool_Dnig_5kb_R2.fastq
JUMP= l3 9000 2200 /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_2.Pool_Dnig_10kb_R1.fastq /scratch/c770/c7701100/Dnig_Genome_reads/HI.2079.005.Index_2.Pool_Dnig_10kb_R2.fastq
END