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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
   Contig # N50 Genome cov. (%) Contig # N50 Genome cov. (%)
5% TAR-VIR 11 920 27.3 97 3643 82.3
  SGA 14 645 26.8 63 675 68.4
  SPAdes 5 1177 27.6 15 3636 79.6
  SAVAGE 13 698 21.6 49 806 40.4
10% TAR-VIR 61 794 67.4 31 2635 84.0
  SGA 26 663 56.4 72 706 69.5
  SPAdes 15 1251 65.4 19 3373 79.3
  SAVAGE 30 631 40.6 32 915 26.5
15% TAR-VIR 97 939 80.9 14 3579 83.1
  SGA 56 617 57.7 74 722 70.2
  SPAdes 20 1689 77.6 16 3986 81.0
  SAVAGE 32 639 29.9 24 999 27.6
20% TAR-VIR 38 1852 84.5 77 5678 86.4
  SGA 78 661 59.5 374 537 64.5
  SPAdes 23 2,710 83.8 10 4830 84.6
  SAVAGE 19 671 19.1 15 823 5.5
  1. ‘cov.’ is the abbreviation for ‘coverage’. The default assembly component in TAR-VIR is PEHaplo