NextDenovo
stable
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Parameter Reference
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Benchmark
CHM13hTERT human cell line with 120x Oxford Nanopore data
Arabidopsis thaliana with 192X PacBio CLR data (~1% heterozygosity)
Drosophila melanogaster with 69X Oxford Nanopore data
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NextDenovo
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Index
B
|
C
|
D
|
G
|
I
|
J
|
K
|
M
|
N
|
P
|
R
|
S
|
T
|
U
|
W
B
blocksize = 10g
command line option
C
check_alive = auto
command line option
command line option
blocksize = 10g
check_alive = auto
correction_options = -p 10
deltmp = yes
genome_size = 1g
input_fofn = input.fofn
input_type = raw
job_id_regex = auto
job_prefix = nextDenovo
job_type = sge
kill = auto
minimap2_options_cns = -t 8 -k17 -w17
minimap2_options_map = -t 10
minimap2_options_raw = -t 10
nextgraph_options = -a 1
nodelist = avanode.list.fofn
pa_correction = 3
parallel_jobs = 10
read_cutoff = 1k
read_type = {clr, hifi, ont}
rerun = 3
rewrite = no
seed_cutfiles = 5
seed_cutoff = 0
seed_depth = 45
sort_options = -m 40g -t 10
submit = auto
task = <all, correct, assemble>
use_drmaa = no
usetempdir = /tmp/test
workdir = 01.workdir
correction_options = -p 10
command line option
D
deltmp = yes
command line option
G
genome_size = 1g
command line option
I
input_fofn = input.fofn
command line option
input_type = raw
command line option
J
job_id_regex = auto
command line option
job_prefix = nextDenovo
command line option
job_type = sge
command line option
K
kill = auto
command line option
M
minimap2_options_cns = -t 8 -k17 -w17
command line option
minimap2_options_map = -t 10
command line option
minimap2_options_raw = -t 10
command line option
N
nextgraph_options = -a 1
command line option
nodelist = avanode.list.fofn
command line option
P
pa_correction = 3
command line option
parallel_jobs = 10
command line option
R
read_cutoff = 1k
command line option
read_type = {clr, hifi, ont}
command line option
rerun = 3
command line option
rewrite = no
command line option
S
seed_cutfiles = 5
command line option
seed_cutoff = 0
command line option
seed_depth = 45
command line option
sort_options = -m 40g -t 10
command line option
submit = auto
command line option
T
task = <all, correct, assemble>
command line option
U
use_drmaa = no
command line option
usetempdir = /tmp/test
command line option
W
workdir = 01.workdir
command line option
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