Genome assembly of the autotetraploid plant
fengyuanli304 opened this issue · comments
Question or Expected behavior
Genome assembly of the autotetraploid plant
Hi, I have recently assembled a genome using nanopore reads, but the results are not good. It may result from its autotetraploidy. Could you please give me some suggestions? Thank you very much.
- nextdenovo + nextpolish
Type Length (bp) Count (#)
N10 3398628 14
N20 2568560 32
N30 1871279 58
N40 1356392 91
N50 939240 138
N60 640978 207
N70 451803 308
N80 316553 449
N90 218120 654
Min. 33288 -
Max. 5440223 -
Ave. 528507 -
Total 538020557 1018
C:96.7%[S:72.4%,D:24.3%],F:0.7%,M:2.6%,n:1375
1329 Complete BUSCOs (C)
995 Complete and single-copy BUSCOs (S)
334 Complete and duplicated BUSCOs (D)
10 Fragmented BUSCOs (F)
36 Missing BUSCOs (M)
1375 Total BUSCO groups searched
2) wtdbg2 + nextpolish
Type Length (bp) Count (#)
N10 7117562 7
N20 5320460 16
N30 3664794 29
N40 1774681 51
N50 816375 95
N60 316343 206
N70 151485 470
N80 79657 986
N90 35990 2038
Min. 2066 -
Max. 11154505 -
Ave. 101844 -
Total 560244256 5501
C:90.9%[S:80.6%,D:10.3%],F:1.7%,M:7.4%,n:1375
1250 Complete BUSCOs (C)
1108 Complete and single-copy BUSCOs (S)
142 Complete and duplicated BUSCOs (D)
24 Fragmented BUSCOs (F)
101 Missing BUSCOs (M)
1375 Total BUSCO groups searched
- necat4 + nextpolish
Type Length (bp) Count (#)
N10 1255211 77
N20 940996 191
N30 758574 333
N40 617986 509
N50 508059 724
N60 416166 985
N70 319953 1315
N80 236195 1754
N90 146935 2391
Min. 504 -
Max. 2499020 -
Ave. 288546 -
Total 1204105988 4173
C:97.0%[S:27.5%,D:69.5%],F:0.9%,M:2.1%,n:1375
1333 Complete BUSCOs (C)
378 Complete and single-copy BUSCOs (S)
955 Complete and duplicated BUSCOs (D)
13 Fragmented BUSCOs (F)
29 Missing BUSCOs (M)
1375 Total BUSCO groups searched
- canu (corrected) +smartdenovo +nextpolish
Type Length (bp) Count (#)
N10 2180472 18
N20 1526697 47
N30 1236412 85
N40 941656 133
N50 780034 193
N60 584817 269
N70 442020 371
N80 288149 518
N90 150110 760
Min. 9906 -
Max. 4119799 -
Ave. 367003 -
Total 515272840 1404
C:96.9%[S:73.6%,D:23.3%],F:0.5%,M:2.6%,n:1375
1332 Complete BUSCOs (C)
1012 Complete and single-copy BUSCOs (S)
320 Complete and duplicated BUSCOs (D)
7 Fragmented BUSCOs (F)
36 Missing BUSCOs (M)
1375 Total BUSCO groups searched
Which one is more suitable for this autotetraploid plant?
I choose the result of nextdenovo + nextpolish for downstream analyses. After removing haplotigs and contig overlaps by purge_dups, I got a smaller genome size.
contigs 598
Largest contig 5440223
Total length 389747736
GC (%) 34.54
N50 1536005
N75 638325
L50 77
L75 176
N's per 100 kbp 0.22
C:92.8%[S:81.2%,D:11.6%],F:1.8%,M:5.4%,n:1375
1275 Complete BUSCOs (C)
1116 Complete and single-copy BUSCOs (S)
159 Complete and duplicated BUSCOs (D)
25 Fragmented BUSCOs (F)
75 Missing BUSCOs (M)
1375 Total BUSCO groups searched
How can I improve this result?
Waiting for your reply.
Operating system
CentOS Linux release 7.6.1810
GCC
What version of GCC are you using?
4.8.5 20150623 (Red Hat 4.8.5-36)
Python
What version of Python are you using?
python2.7.18
NextDenovo
What version of NextDenovo are you using?
nextdenovo2.4
Additional context (Optional)
Add any other context about the problem here.
