Index

C

check_alive = auto command line option command line option check_alive = auto deltmp = yes genome = genome.fa genome_size = auto hifi_fofn = ./hifi.fofn hifi_minimap2_options = -x map-pb -t {multithread_jobs} hifi_options = -min_read_len 1k -max_depth 100 job_id_regex = auto job_prefix = nextPolish job_type = sge kill = auto lgs_fofn = ./lgs.fofn lgs_minimap2_options = -x map-pb -t {multithread_jobs} lgs_options = -min_read_len 1k -max_depth 100 multithread_jobs = 5 parallel_jobs = 6 polish_options = -p {multithread_jobs} rerun = 3 rewrite = no sgs_fofn = ./sgs.fofn sgs_options = -max_depth 100 -bwa submit = auto task = best use_drmaa = no workdir = 01_rundir

D

deltmp = yes command line option

G

genome = genome.fa command line option

genome_size = auto command line option

H

hifi_fofn = ./hifi.fofn command line option hifi_minimap2_options = -x map-pb -t {multithread_jobs} command line option

hifi_options = -min_read_len 1k -max_depth 100 command line option

J

job_id_regex = auto command line option job_prefix = nextPolish command line option

job_type = sge command line option

K

kill = auto command line option

L

lgs_fofn = ./lgs.fofn command line option lgs_minimap2_options = -x map-pb -t {multithread_jobs} command line option

lgs_options = -min_read_len 1k -max_depth 100 command line option

M

multithread_jobs = 5 command line option

P

parallel_jobs = 6 command line option

polish_options = -p {multithread_jobs} command line option

R

rerun = 3 command line option

rewrite = no command line option

S

sgs_fofn = ./sgs.fofn command line option sgs_options = -max_depth 100 -bwa command line option

submit = auto command line option

T

task = best command line option

U

use_drmaa = no command line option

W

workdir = 01_rundir command line option