necat

#BSUB -J necat
#BSUB -n 1
#BSUB -R span[hosts=1]
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -q normal

module load NECAT/20200803
date
necat.pl correct oleracea_config.txt
necat.pl assemble  oleracea_config.txt
necat.pl bridge  oleracea_config.txt
date

PROJECT=oleracea
ONT_READ_LIST=read_list.txt
GENOME_SIZE=630000000
THREADS=8
MIN_READ_LENGTH=3000
OVLP_FAST_OPTIONS="-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000"
OVLP_SENSITIVE_OPTIONS="-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000"
CNS_FAST_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0"
CNS_SENSITIVE_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0"
TRIM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400"
ASM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400"
NUM_ITER=2
CNS_OUTPUT_COVERAGE=45
CLEANUP=0
USE_GRID=true
GRID_NODE=80
FSA_OL_FILTER_OPTIONS="--max_overhang=-1 --min_identity=-1 --coverage=40"
FSA_ASSEMBLE_OPTIONS=""
FSA_CTG_BRIDGE_OPTIONS="--dump --read2ctg_min_identity=80 --read2ctg_min_coverage=4 --read2ctg_max_overhang=500 --read_min_length=5000 --ctg_min_length=1000 --read2ctg_min_aligned_length=5000 --select_branch=best"