## Config file used for FALCON assembly.
[General]
# list of files of the initial bas.h5 files
input_fofn = input.fofn

input_type = raw

# The length cutoff used for seed reads used for initial mapping
length_cutoff = -1
genome_size = 14200000
seed_coverage = 30

# The length cutoff used for seed reads usef for pre-assembly
length_cutoff_pr = 1000

pa_daligner_option   = -e.70 -l2000 -k18 -h240 -w8 -s100
ovlp_daligner_option = -e.96 -l1000 -k24 -h240 -w6 -s100
pa_HPCdaligner_option   = -v -B128 -M48
ovlp_HPCdaligner_option = -v -B128 -M48

pa_DBsplit_option = -x500 -s400
ovlp_DBsplit_option = -s400

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 2 --max_n_read 200 --n_core 12
falcon_sense_skip_contained = True

overlap_filtering_setting = --max-diff 100 --max-cov 100 --min-cov 2 --n-core 24

[job.defaults]
job_type = local

use_tmpdir = /lscratch
pwatcher_type = blocking
job_type = string
submit = bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}

NPROC = 48
njobs = 1
MB = 50000
[job.step.da]
[job.step.pda]
[job.step.la]
[job.step.pla]
[job.step.cns]
[job.step.asm]