Table 1 Summary of evaluation for assembled genomes of C. variabilis under various conditions using various indexes
From: De novo assembly of middle-sized genome using MinION and Illumina sequencers
Reference | Short-read | Long | Hybrid | |||||
|---|---|---|---|---|---|---|---|---|
ABrujin | Abrujin-polished | Miniasm | Canu | SPAdes-hybrid | MaSuRCA | |||
Assembly quality | ||||||||
# contigs (> = 0 bp) | 414 | 13,015 | 259 | 170 | 492 | 2400 | 10,635 | 302 |
# contigs (> = 1000 bp) | 414 | 1870 | 259 | 170 | 492 | 2399 | 1079 | 302 |
# contigs (> = 5000 bp) | 134 | 1171 | 259 | 170 | 484 | 1909 | 772 | 241 |
# contigs (> = 10,000 bp) | 82 | 950 | 259 | 170 | 438 | 1158 | 664 | 196 |
# contigs (> = 25,000 bp) | 55 | 642 | 259 | 170 | 335 | 141 | 511 | 150 |
# contigs (> = 50,000 bp) | 44 | 348 | 225 | 164 | 243 | 18 | 359 | 134 |
Total length (> = 0 bp) | 46,159,515 | 58,108,416 | 44,173,773 | 45,397,519 | 42,468,310 | 27,800,588 | 58,637,084 | 46,674,734 |
Total length (> = 1000 bp) | 46,159,515 | 56,312,404 | 44,173,773 | 45,397,519 | 42,468,310 | 27,799,589 | 57,237,973 | 46,674,734 |
Total length (> = 5000 bp) | 45,602,804 | 54,680,763 | 44,173,773 | 45,397,519 | 42,437,055 | 26,338,534 | 56,523,201 | 46,494,724 |
Total length (> = 10,000 bp) | 45,222,671 | 53,103,981 | 44,173,773 | 45,397,519 | 42,054,109 | 20,603,401 | 55,758,312 | 46,162,375 |
Total length (> = 25,000 bp) | 44,846,071 | 48,059,147 | 44,173,773 | 45,397,519 | 40,395,860 | 5,591,416 | 53,252,484 | 45,478,395 |
Total length (> = 50,000 bp) | 44,435,177 | 37,767,367 | 42,798,957 | 45,170,192 | 36,950,227 | 1,766,192 | 47,753,927 | 44,916,352 |
# contigs | 414 | 2540 | 259 | 170 | 492 | 2400 | 1479 | 302 |
Largest contig | 3,119,887 | 765,833 | 1,514,322 | 1,157,783 | 685,202 | 327,336 | 770,020 | 2,552,940 |
Total length | 46,159,515 | 56,771,972 | 44,173,773 | 45,397,519 | 42,468,310 | 27,800,588 | 57,502,328 | 46,674,734 |
GC (%) | 67.1 | 67.9 | 64.4 | 65.8 | 64.8 | 62.2 | 67.8 | 67.1 |
N50 | 1,469,606 | 77,546 | 250,313 | 376,772 | 161,216 | 14,421 | 130,737 | 501,441 |
N75 | 953,202 | 36,956 | 137,022 | 228,146 | 84,461 | 9866 | 66,441 | 250,951 |
L50 | 12 | 195 | 54 | 35 | 77 | 599 | 127 | 23 |
L75 | 21 | 462 | 113 | 75 | 166 | 1183 | 279 | 55 |
# N’s per 100 kbp | 8547 | 27 | 0 | 0 | 0 | 0 | 139 | 13 |
Alignment to reference | ||||||||
Coverage | – | 92.21% | 94.68% | 99.73% | 90.23% | 26.09% | 93.76% | 100.77% |
Identity | – | 89.19% | 21.16% | 69.82% | 14.69% | 2.56% | 89.96% | 97.23% |
Gene model quality | ||||||||
ECR | 82.90% | 86.50% | 1.30% | 10.90% | 0.00% | 0.00% | 86.80% | 88.50% |
RNA-seq Mapping Rate | 90.32% | 95.81% | 23.08% | 56.81% | 18.68% | 5.74% | 96.25% | 95.06% |