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Table 5 ContigExtender results on Human metagenome datasets using MetaSPAdes as seed contigs

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

Contig ID Library Meta SPAdes (bp) Contig Extender (bp) Gained length (bp) Gained (%) Aligned (bp) Aligned (%) Genome Genome size (bp) Gained genome (%)
1 Amazon-4B 7560 10,034 2474 33 7493 75 Norwalk_virus (NC_040876.1) 7521 33
2 Amazon-17D 7912 8329 417 5 7862 94 Husavirus_sp. (NC_032480.1) 8856 5
3 Amazon-3D 1537 7676 6139 399 7678 100 Husavirus_sp. (NC_032480.1) 8856 69
4 Amazon-3D 3776 7530 3754 99 7532 100 Husavirus_sp. (NC_032480.1) 8856 42
5 Amazon-3D 2165 7530 5365 248 7532 100 Husavirus_sp. (NC_032480.1) 8856 61
6 Amazon-S10-CNI-055 1671 3258 1587 95 3242 100 Betapapillomavirus_1 (NC_001531.1) 7746 20
7 Amazon-S10-CNI-055 1710 3258 1548 91 3242 100 Betapapillomavirus_1 (NC_001531.1) 7746 20
8 Amazon-6D 2151 2772 621 29 2681 97 Human_cosavirus (NC_023984.1) 7802 8
9 12-110034-veqrpcr 2339 5237 2898 124 5233 100 Hepacivirus_C(NC_004102.1) 9646 30
10 47210-feces 2436 4637 2201 90 4444 96 Escherichia_virus_AKFV33 (NC_017969.1) 108,853 2
11 47210-feces 2436 3572 1136 47 3572 100 Escherichia_virus_T5 (NC_005859.1) 121,750 1
12 12-110034-veqrpcr 2424 3157 733 30 3121 99 Hepacivirus_C (NC_004102.1) 9646 8
13 12-110,034-veqrpcr 2424 3156 732 30 3121 99 Hepacivirus_C (NC_004102.1) 9646 33
  1. Columns 3–11 are: 3) seed contig length generated by MetaSPAdes; 4) extended contig length from seed contig; 5) gained length from ContigExtender (column 4 subtracted by column 3); 6) Gained length as percentage of seed contig (column 5 divided by column 3); 7) the largest contiguous segment length of extended contig that are aligned to reference genome; 8) percentage of the alignment segment of the extend contig; 9) reference viral genome; 10) viral genome size; 11) gained length from ContigExtender as percentage of viral genome (column 5 divided by column 10). Note that PRICE, GenSeed, and Kollector did not extend any seed contigs in this set, so their columns are omitted