Table 5 Assembly statistics and NLR-Parser evaluation of the assemblies: Canu assembly (nanopolished and not nanopolished) using MinION 2D pass data, Canu using PacBio RoI, HGAP using PacBio RoI and Geneious PacBio RoI
Canu MinION | Canu MinION (nanopolish) | Canu PacBio | HGAP | Geneious | |
|---|---|---|---|---|---|
Number of contigs | 1085 | 1085 | 1483 | 1460 | 837 |
Minimal contig length [bp] | 1568 | 1695 | 1008 | 517 | 3882 |
Contig N80 [bp] | 4873 | 4958 | 4464 | 3949 | 7775 |
Contig N50 [bp] | 8089 | 8230 | 6817 | 7149 | 10,935 |
Contig N20 [bp] | 13,963 | 14,185 | 12,785 | 11,796 | 18,321 |
Mean contig size | 12,167 | 12,366 | 10,099 | 9353 | 13,929 |
Maximal contig length (bp) | 132,431 | 134,631 | 59,085 | 85,187 | 55,450 |
Sum of bp assembled | 7,606,604 | 7,749,213 | 9,835,757 | 8,307,997 | 9,008,910 |
NLR-Parser hits | 584 | 608 | 557 | 667 | 586 |
NLR-Parser hits scored as partial | 308 | 332 | 324 | 372 | 257 |
% NLR-Parser hits scored as partial | 52.74% | 54.60% | 58.35% | 55.69% | 43.78% |
NLR-Parser hits scored as complete | 275 | 276 | 231 | 295 | 329 |
% NLR-Parser hits scored as complete | 47.26% | 45.39% | 41.65% | 44.31% | 56.21% |