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Table 3 ContigExtender results on NIBSC datasets using MetaSPAdes assembly outputs as seed contigs

From: ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

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
  1. 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