Table 1. Comparison of assembly contiguity statistics in three ducks, chicken and zebra finch genomes
Index | Peking duck SKLA1.0 | Peking duck ZJU1.0 | Peking duck BGI 1.0 | Chicken GRCg6a | Zebra finch bTaeGut1.4.pri |
|---|---|---|---|---|---|
Assembly size (Mb) | 1159.66 | 1188.53 | 1105.04 | 1065.36 | 1056.27 |
Chromosome | 40 | 33 | 0 | 34 | 41 |
Sequencing technology | Illumina Nanopore Ultra-long Bionano Hi-C | Illumina 10 X PacBio Bionano Hi-C | Illumina | PacBio | Arima Illumina PacBio HIFI Bionano Hi-C |
Coverage (X) | 117 Illumina 71 Nanopore 24 Ultra-long 222 Bionano 234 Hi-C | 92 Illumina 142 10X 143 Pacbio 56 Bionano 82 Hi-C | 64 Illumina | 82 PacBio | 242 Arima 134 Illumina 396 10X 321 Pacbio 335 HIFI 2281 Bionano |
Assembler | Nextdenovo SOLVE Juicer 3D-DNA Juicebox | FALCON Scaff10X runBNG SALSA2 | SOAPdenovo | FALCON | FALCON Scaff10X Solve SALSA2 |
Contig N50 (Mb) | 32.90 | 5.68 | 0.026 | 17.66 | 8.96 |
Contig L50 | 9 | 57 | 11206 | 19 | 32 |
Max contig (Mb) | 160.37 | 28.52 | 0.26 | 65.78 | 65.49 |
No. contigs | 151 | 1161 | 227448 | 1403 | 551 |
Scaffold N50 (Mb) | 76.57 | 76.27 | 1.23 | 20.79 | 70.98 |
Scaffold L50 | 5 | 5 | 268 | 12 | 6 |
No. scaffolds | 134 | 756 | 78487 | 525 | 199 |