Closed A-J-F-Mackintosh closed 2 years ago
Could you provide how about the assembly result with genome_size=350Mb?
Yes, once it is finished I will post the results here.
Alex
ok, after that, maybe I can provide some suggestions.
Hi,
With genome_size=350Mb
the result is very good. It will need haplotig purging but that is fine.
Reads
Types Count (#) Length (bp)
N10 44772 43676
N20 105555 35441
N30 177975 30403
N40 261524 26480
N50 358097 22673
N60 472811 18758
N70 614194 14909
N80 797644 11106
N90 1060882 7117
Types Count (#) Bases (bp) Depth (X)
Raw 1802948 23747597071 67.85
Filtered 124762 57217197 0.16
Clean 1678186 23690379874 67.69
*Suggested seed_cutoff (genome size: 350.00Mb, expected seed depth: 45, real seed depth: 45.00): 16257 bp
Contigs
Type Length (bp) Count (#)
N10 10837787 5
N20 7882032 13
N30 5921275 22
N40 4274629 35
N50 3531405 53
N60 2987626 73
N70 2214973 98
N80 1443093 134
N90 702402 196
Min. 17033 -
Max. 16126662 -
Ave. 1401976 -
Total 663135083 473
Could still be worth trying genome_size=700Mb
? Or reducing seed_depth
to 30?
Best,
Alex
you can try nextgraph_options = -A
or nextgraph_options =-q 5 or 10
or try seed_depth=40
, but I am not sure whether these opts will improve the assembly result.
Hi,
I tried seed_depth = 40
along with nextgraph_options = -a 1 -A
. This generated a larger assembly (754Mb) with similar contiguity as before.
I will use my first assembly as this will be easier to purge.
Thank you for the advice nonetheless.
Best,
Alex
Hi,
First of all, thank you for your work on this really nice assembler.
I have had success using NextDenovo v2.4.0 to assemble some insect genomes. I will soon try to assemble a 350Mb genome, where heterozygosity is 3.5%, from 68X Pacbio CLR data.
Would you recommend changing any particular parameters? For example, I could set the genome size as 700Mb (diploid) to reduce the minimum seed length. My thinking is that this would provide more information per-haplotype and so less small bubbles will appear in the graph.
Many thanks,
Alex