Table 5 Assembly evaluation results on aligned and recruited reads using the genomes of HBV, HCV, and HPgV as references
From: TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data
Align | Tool | Bowtie2 aligned | Bowtie2 Recruited | ||||
|---|---|---|---|---|---|---|---|
| Â | Â | Contig # | N50 | Genome cov. (%) | Contig # | N50 | Genome cov. (%) |
5% | TAR-VIR | 11 | 920 | 27.3 | 97 | 3643 | 82.3 |
| Â | SGA | 14 | 645 | 26.8 | 63 | 675 | 68.4 |
| Â | SPAdes | 5 | 1177 | 27.6 | 15 | 3636 | 79.6 |
| Â | SAVAGE | 13 | 698 | 21.6 | 49 | 806 | 40.4 |
10% | TAR-VIR | 61 | 794 | 67.4 | 31 | 2635 | 84.0 |
| Â | SGA | 26 | 663 | 56.4 | 72 | 706 | 69.5 |
| Â | SPAdes | 15 | 1251 | 65.4 | 19 | 3373 | 79.3 |
| Â | SAVAGE | 30 | 631 | 40.6 | 32 | 915 | 26.5 |
15% | TAR-VIR | 97 | 939 | 80.9 | 14 | 3579 | 83.1 |
| Â | SGA | 56 | 617 | 57.7 | 74 | 722 | 70.2 |
| Â | SPAdes | 20 | 1689 | 77.6 | 16 | 3986 | 81.0 |
| Â | SAVAGE | 32 | 639 | 29.9 | 24 | 999 | 27.6 |
20% | TAR-VIR | 38 | 1852 | 84.5 | 77 | 5678 | 86.4 |
| Â | SGA | 78 | 661 | 59.5 | 374 | 537 | 64.5 |
| Â | SPAdes | 23 | 2,710 | 83.8 | 10 | 4830 | 84.6 |
| Â | SAVAGE | 19 | 671 | 19.1 | 15 | 823 | 5.5 |