Table 6 Assembly comparison after spliting by continuous fragments
From: LDscaff: LD-based scaffolding of de novo genome assemblies
Assembly composition | SOAPdenovo + LDscaff | SOAPdenovo + HiC | SOAPdenovo + LDscaff + HiC |
|---|---|---|---|
Assembly size | 2266537396 | 2252886107 | 1797011536 |
No. scaffolds | 382 | 647 | 123 |
N50 size | 32092974 | 58665385 | 1254064180 |
Misassemblies | 2426 | 4852 | 2162 |
Contig misassemblies | 2426 | 4852 | 2162 |
   c. relocations | 589 | 1231 | 524 |
   c. translocations | 1678 | 3298 | 1490 |
   c. inversions | 159 | 323 | 148 |
Scaffold misassemblies | 0 | 0 | 0 |
   s. relocations | 0 | 0 | 0 |
   s. translocations | 0 | 0 | 0 |
   s. inversions | 0 | 0 | 0 |
Misassembled contigs | 1528 | 3120 | 1384 |
Misassembled contigs length | 71602181 | 144952053 | 67084793 |
Local misassemblies | 28366 | 58360 | 27273 |
Unaligned mis. contigs | 117 | 203 | 102 |
Mismatches | 13257465 | 27321894 | 12732835 |
Indels | 1249703 | 2585745 | 1204396 |
   Indels (\(\le\) 5 bp) | 1041691 | 2156454 | 1004988 |
   Indels (> 5 bp) | 208012 | 429291 | 199408 |
Indels length | 5760596 | 11919093 | 5519229 |