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 |