Table 3 BUSCO scores following different methods of genome sequence correction. The percentage of complete USCOs together with the number of single, duplicated, fragmented (Frag) or missing USCO predicted from the uncorrected genome sequence, or the sequence after processing by different methods (see ‘Methods’ for details). The figures for the WTSI reference are shown for comparison. The default analysis mode is the short one. In the long mode, an optimization of the BUSCO sub-program Augustus is used for self-training, substantially increasing run times
From: De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
| Â | Short BUSCO | Long BUSCO | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Description | Complete (%) | Single (n) | Duplicated (n) | Fragmented (n) | Missing (n) | Complete (%) | Single (n) | Duplicated (n) | Fragmented (n) | Missing (n) |
Uncorrected (Canu only) | 49.2 | 437 | 46 | 128 | 371 | 65.0 | 585 | 53 | 122 | 222 |
Nanopolish | Â | Â | Â | Â | Â | 85.4 | 733 | 106 | 73 | 70 |
Bowtie2 + Pilon | 75.6 | 630 | 112 | 95 | 145 | 85.1 | 709 | 127 | 72 | 74 |
HISAT2 + Pilon | 74.7 | 618 | 116 | 101 | 147 | 81.5 | 679 | 122 | 83 | 98 |
Trinity# [de novo] | 90.8 90.7 | 681 441 | 211 450 | 65 64 | 25 27 | 91.3 | 446 | 451 | 59 | 26 |
Trinity# [genome-guided] | 88.4 88.2 | 316 304 | 552 562 | 63 61 | 51 55 | 88.5 | 305 | 564 | 58 | 55 |
Trinity# [Expression-filtered] | 87.9 87.7 | 644 613 | 219 248 | 58 60 | 61 61 | 88.3 | 618 | 249 | 55 | 60 |
Trinity# [collapsed] | 87.2 87 | 786 791 | 71 64 | 58 63 | 67 64 | 87.6 | 796 | 64 | 57 | 65 |
WTSI reference | 73.1 | 677 | 41 | 133 | 131 | 80.6 | 748 | 43 | 125 | 66 |