Table 2 Detection of viruses in various viral metagenomics datasets.
From: VIP: an integrated pipeline for metagenomics of virus identification and discovery
Platform | Data source | Sample type | Independent confirmatory testing results | VIP results | Genome Coverage (%) | Total reads | Number of reads (%) |
|---|---|---|---|---|---|---|---|
HiSeq 2000 | SRR453448 | serum | Dengue virus 2 | Dengue virus 2 | 99.14 | 1,678,692 | 64,778(3.86) |
HiSeq 2000 | SRR453458 | serum | Hepatitis A virus | Hepatitis A virus | 57.15 | 446,961 | 2,315(0.52) |
HiSeq 2500 | SRR1106123 | serum | Hepatitis C virus | Hepatitis C virus | 100.00 | 11,204,134 | 108,274(0.97) |
Hepatitis G virus | Hepatitis G virus | 100.00 | 11,204,134 | 751,691(6.71) | |||
MiSeq | SRR1106548 | plasma | HIV | HIV | 96.61 | 2,030,011 | 29,528(1.45) |
Genome Analyzer IIx | SRR1106553 | nasal swab | H1N1 | H1N1 | 98.25 | 773,835 | 12,613(1.63) |
Ion Torrent PGM | SRR1170820 | nasal swab | BoCV | BoCV | 99.90 | 173,472 | 9,767(5.63) |
BVDV | 86.13 | 173,472 | 387(0.22) | ||||
Ion Torrent PGM | SRR1170797 | buffy coat | BVDV | BVDV | 100.00 | 95,452 | 33,454(35.05) |
Ion Torrent PGM | In-house-1 | serum | real-time PCR | Dengue virus 1 | 96.32 | 206,444 | 1,514(0.73) |
454 GS Junior | In-house-2 | stool | N/A | Torque teno mini virus 5 | 98.89 | 290,647 | 1,226(0.42) |
N/A | Pepper mild mottle virus | 98.52 | 290,647 | 1,758(0.60) | |||
real-time PCR | Human parechovirus 3 | 97.80 | 290,647 | 595(0.20) | |||
real-time PCR | Norovirus GII | 96.28 | 290,647 | 372(0.13) | |||
real-time PCR | Human echovirus 9 | 84.83 | 290,647 | 128(0.04) | |||
Hiseq 2000 | In-house-3 | swab | PCR | RSV | 98.41 | 5,147,814 | 139,970(2.72) |
Nest PCR | Human coronavirus 229E | 17.00 | 5,147,814 | 262(0.01) |
