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Table 2 Assembly results on SARS-CoV aligned and recruited metagenomic data

From: TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

Aligned Tool # Contigs N50 Genomes covered (%) Mismatch rate (%)
Bowtie2 L,0,-0.9 TAR-VIR 58 505 19.7 0.02
  SGA 56 505 20.1 0.03
  SPAdes 34 569 12.9 0.16
  SAVAGE 54 455 17.5 0.0
Recruited Tool # Contigs N50 Genomes covered (%) Mismatch rate (%)
  TAR-VIR 7 29,676 98.9 0.0
  SGA 13 26,729 98.9 0.0
  SPAdes 14 15,882 92.1 0.51
Bowtie2 L,0,-0.9 SAVAGE 22 12,445 97.0 0.0
Aligned Tool # Contigs N50 Genomes covered (%) Mismatch rate (%)
  TAR-VIR 84 1192 55.1 0.0
  SGA 85 1027 56.5 0.0
  SPAdes 67 1012 44.6 0.12
BWA B:1 SAVAGE 68 669 32.3 0.0
Recruited Tool # Contigs N50 Genomes covered (%) Mismatch rate (%)
BWA B:1 TAR-VIR 6 29,706 99.5 0.0
  SGA 18 12,638 99.5 0.0
  SPAdes 21 10,353 89.2 0.39
  SAVAGE 56 5140 89.3 0.0
  1. The default assembly tool in TAR-VIR is PEHaplo. Definition of the metrics can be found in “Data properties and evaluation metrics” section