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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

  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       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
  1. USCO universal single-copy ortholog (genes), WTSI Wellcome Trust Sanger Institute
  2. #Statistics in italics are from transcript mode BUSCO