cfg_arab_clr

project=arab
reads= $READS
genome_size=130000000
threads=48
cleanup=1
grid=local

prep_min_length=3000
prep_output_coverage=80

corr_iterate_number=1
corr_block_size=4000000000
corr_filter_options=--filter0=:al=5000:alr=0.5:aal=8000:aalr=0.5:oh=2000:ohr=0.2
corr_correct_options=--score=weight:lc=10 --aligner diff --filter1 oh=1000:ohr=0.01
corr_rd2rd_options=-x ava-pb
corr_output_coverage=80

align_block_size=4000000000
align_rd2rd_options=-X -g3000 -w30 -k19 -m100 -r500
align_filter_options=--filter0=l=3000:al=3000:alr=0.5:aalr=0.5:oh=1000:ohr=0.1 --task=extend --filter1=oh=100:ohr=0.01

asm1_assemble_options=--max_trivial_length 10000

phase_rd2ctg_options=-x map-pb -c -p 0.5 -r 1000
phase_use_reads=1
phase_phase_options= --phase_options icr=0.2
phase_filter_options= --threshold=1000

asm2_assemble_options=--max_trivial_length 10000 --contig_format dual,prialt

polish_use_reads=1
polish_map_options = -x asm20
polish_cns_options =