# quick run configuration file
DATA
PE = pe 500 50 /scratch/user/kasuni91/MaSuRCA/CAA1B_right_mates.fastq /scratch/user/kasuni91/MaSuRCA/CAA1B_left_mates.fastq
NANOPORE = /scratch/user/kasuni91/MaSuRCA/caa1_nanopre_filtered.fastq
END
PARAMETERS
EXTEND_JUMP_READS=0
GRAPH_KMER_SIZE = auto
USE_LINKING_MATES = 0
USE_GRID=0
GRID_ENGINE=SGE
GRID_QUEUE=all.q
GRID_BATCH_SIZE=500000000
LHE_COVERAGE=25
LIMIT_JUMP_COVERAGE = 300
CA_PARAMETERS = cgwErrorRate=0.15 doFragmentCorrection=0
CLOSE_GAPS=1
NUM_THREADS = 20
JF_SIZE = 8000000000
SOAP_ASSEMBLY=0
FLYE_ASSEMBLY=0
END