Table 3.
ContigExtender results on NIBSC datasets using MetaSPAdes assembly outputs as seed contigs
| Contig ID | Meta SPAdes (bp) | Contig Extender (bp) | Gained length (bp) | Gained (%) | Aligned (bp) | Aligned (%) | Viral genome (Accession) | Genome size (bp) | Gained genome (%) | PRICE (bp) | GenSeed (bp) | Kollector (bp) | Depth (x) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4251 | 10,059 | 5808 | 137 | 10,057 | 100 | Human_rubulavirus_2 (NC_003443.1) | 15,646 | 37 | 54 | |||
| 2 | 3114 | 8315 | 5201 | 167 | 8288 | 100 | Human_mastadenovirus_C (NC_001405.1) | 35,937 | 14 | 31 | |||
| 3 | 4705 | 6841 | 2136 | 45 | 6814 | 100 | Human_mastadenovirus_C (NC_001405.1) | 35,937 | 6 | 36 | |||
| 4 | 4118 | 5099 | 981 | 24 | 5057 | 99 | Human_mastadenovirus_C (NC_001405.1) | 35,937 | 3 | 36 | |||
| 5 | 2818 | 5063 | 2245 | 80 | 5062 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 2 | 14 | |||
| 6 | 2234 | 4671 | 2437 | 109 | 4675 | 100 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 1 | 28 | |||
| 7 | 1784 | 4224 | 2440 | 137 | 4224 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 2 | 11 | |||
| 8 | 3944 | 4171 | 227 | 6 | 4149 | 99 | Human_mastadenovirus_C (NC_001405.1) | 35,937 | 1 | 29 | |||
| 9 | 3051 | 4098 | 1047 | 34 | 4092 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 1 | 16 | |||
| 10 | 3158 | 4029 | 871 | 28 | 3575 | 89 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 0 | 42 | |||
| 11 | 3462 | 3964 | 502 | 15 | 3961 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 0 | 23 | |||
| 12 | 1789 | 3666 | 1877 | 105 | 3665 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 2 | 14 | |||
| 13 | 1761 | 3379 | 1618 | 92 | 3319 | 98 | Rotavirus_A (NC_011507.2) | 3302 | 49 | 3403 | 126 | ||
| 14 | 1759 | 3292 | 1533 | 87 | 2552 | 78 | Bat_rotavirus (NC_040413.1) | 2649 | 58 | 2274 | 2101 | 267 | |
| 15 | 2748 | 3140 | 392 | 14 | 3146 | 100 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 0 | 24 | |||
| 16 | 2861 | 3115 | 254 | 9 | 3115 | 100 | Human_respirovirus_1 (NC_003461.1) | 15,600 | 2 | 29 | |||
| 17 | 2664 | 3016 | 352 | 13 | 3016 | 100 | Human_mastadenovirus_C (NC_001405.1) | 35,937 | 1 | 25 | |||
| 18 | 1525 | 2839 | 1314 | 86 | 2840 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 1 | 7 | |||
| 19 | 1958 | 2616 | 658 | 34 | 2612 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 1 | 27 | |||
| 20 | 1789 | 2213 | 424 | 24 | 2213 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 0 | 8 | |||
| 21 | 1889 | 2154 | 265 | 14 | 2154 | 100 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 0 | 29 | |||
| 22 | 1881 | 2093 | 212 | 11 | 2093 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 0 | 19 | |||
| 23 | 1748 | 2001 | 253 | 14 | 1996 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 0 | 14 | |||
| 24 | 1699 | 1931 | 232 | 14 | 1931 | 100 | Human_alphaherpesvirus_3 (NC_001348.1) | 124,884 | 0 | 21 | |||
| 25 | 1505 | 1846 | 341 | 23 | 1847 | 100 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 0 | 27 | |||
| 26 | 1508 | 1768 | 260 | 17 | 1770 | 100 | Human_betaherpesvirus_5 (NC_006273.2) | 235,646 | 0 | 26 |
Columns 2–14 are: 2) seed contig length generated by MetaSPAdes; 3) extended contig length from seed contig; 4) gained length from ContigExtender (column 3 subtracted by column 2); 5) gained length as percentage of seed contig (column 4 divided by column 2); 6) the largest contiguous segment length of extended contig that are aligned to reference genome; 7) percentage of the alignment segment of the extend contig; 8) reference viral genome; 9) viral genome size; 10) gained length from ContigExtender as percentage of viral genome (column 4 divided by column 9); 11) gained extension by PRICE; 12) gained extension by GenSeed; 13) gained extension by Kollector; 14) average sequencing depth of the extended contig. Entries in the PRICE, GenSeed, and Kollector columns are blank if they produced no extension