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How to improve the N50 and reduce contigs numbers? #200

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@cj2jy

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@cj2jy

Hi, I finished an assembly and the result is:

Type Length (bp) Count (#)
N10 22880485 3
N20 10335838 10
N30 6877938 22
N40 5222529 39
N50 3377214 63
N60 1919981 103
N70 927783 178
N80 440773 335
N90 218142 666

Min. 28326 -
Max. 57348206 -
Ave. 742827 -
Total 992417917 1336

run.cfg:

[General]
job_type = slurm
submit = sbatch --cpus-per-task=20 --mem-per-cpu=4g -o {out} -e {err} {script}
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 1
parallel_jobs = 5
input_type = raw
read_type = ont
input_fofn = ./input.fofn
workdir = ./02_rundir

[correct_option]
read_cutoff = 2k
genome_size = 850M
seed_cutoff = 25000
pa_correction = 3
sort_options = -m 20g -t 18
minimap2_options_raw = -t 18
correction_options = -p 18

[assemble_option]
random_round = 20
minimap2_options_cns = -t 18 -k 23 -w 10
nextgraph_options = -a 1 -q 10

What can I do to increase the N50 and reduce the total number of contigs? I want a better result for 3d-DNA.
Looking forward to reply. Thank you.

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