TABLE 1.
VPipe compared with previous tools for data sets of predominantly single virus speciesa
| SRA data set, accession no. | Target virus (length, kb)b | Assembly features | Assembly results by pipeline | ||||
|---|---|---|---|---|---|---|---|
| VPipe | drVM (20) | EDGE (25) | VirMAP (21) | Genome Detective (27) | |||
| SRR1553609 | Ebola virus (18.8–19.0) | Contig count | 1 | n/rd | 1 | 1 | 7 |
| Max. contig (bp) | 18,756 | n/r | 18,600 | 18,728 | 7,509 | ||
| SRR1170797 | Bovine viral diarrhea virus 2 (12.3–12.5) | Contig count | 12 | 1 | 4 | 1 | 2 |
| Max. contig (bp) | 8,726 | 12,224 | 1,602 | 11,699 | 8,481 | ||
| SRR13403396 | Enterovirus D94 (7.3–7.4) | Contig count | 1 | n/r | 1 | 1 | 1 |
| Max. contig (bp) | 7,457 | n/r | 670 | 7,573 | 7,320 | ||
| PiType (Vpipe) | EV-D94 | - | Enterovirus_D | ||||
| SRR13402413 | Enterovirus D70 (∼7.4) | Contig count | 1 | n/r | 1 | 1 | 1 |
| Max. contig (bp) | 7,353 | n/r | 7,248 | 7,395e | 7,390 | ||
| PiType (Vpipe) | EV-D70 | - | Enterovirus_D | ||||
| SRR10298816 | Human parechovirus 3 (7.2–7.3) | Contig count | 1 | n/r | 1 | 1 | 1 |
| Max. contig (bp) | 7,153 | n/r | 332 | 7,252 | 7,157 | ||
| PiType (Vpipe) | PEV-A3 | - | - | ||||
| SRR10298815 | Enterovirus A71 (7.4–7.5) | Contig count | 4 | n/r | 123 | 1 | 2 |
| Max. contig (bp) | 6,952 | n/r | 832 | 7,423 | 4,919 | ||
| PiType (Vpipe) | EV-A71 | - | Enterovirus_A | ||||
| SRR10298813 | Human parechovirus 3 (7.2–7.3) | Contig count | 5 | n/r | 6 | 1 | 7 |
| Max. contig (bp) | 6,273 | n/r | 404 | 7,269 | 2,220 | ||
| PiType (Vpipe) | PeV-A3 | - | - | ||||
| SRR10298814 | Coxsackievirus B5 (7.3–7.4) | Contig count | 2 | n/r | 3 | 1 | 1 |
| Max. contig | 5,137 | n/r | 4,294 | 7,361 | 7,165 | ||
| PiType (Vpipe) | CV-B5 | - | Human echovirus 6 | ||||
| DRR049387 | Human rotavirus A (longest segment ∼3.3) | Contig countc | 11 | 13 | 7 | 11 | 11 |
| Max. contig (bp) | 3,462 | 3,375 | 3,338 | 3,349 | 3,299 | ||
| ERR690519 | Influenza A virus (longest segment ∼2.3) | Contig countc | 8 | 8 | 8 | 8 | 9 |
| Max. contig (bp) | 2,340 | 2,340 | 2,370 | 2,297 | 2,285 | ||
| SRR1106548 | HIV-1 (∼9.7) | Contig count | 8 | 12 | 5 | 8 | 4 |
| Max. contig (bp) | 4,956 | 2,819 | 5,195 | 5,163 | 4,319 | ||
| Microviridae (2.7–37.0) | Contig count | 1 | Not detected | Not detected | 1 | Not detected | |
| Max. contig (bp) | 5,211 | 5,129 | |||||
| GB virus C (9.3–9.4) | Contig count | 84 | Not detected | 53 | 8 | 2 | |
| Max. contig (bp) | 1,612 | 1,639 | 2,004 | 9,102 | |||
| SRR1106123 | Hepatitis C virus (9.6–9.8) | Contig count | 2 | 15 | 2 | 1 | 1 |
| Max. contig (bp) | 5,125 | 2,227 | 7,850 | 9,316 | 9,418 | ||
| GB virus C (9.3–9.4) | Contig count | 2 | 159 | 10 | 1 | 2 | |
| Max. contig (bp) | 9,013 | 825 | 5,711 | 9,276 | 9,295 | ||
a
Strain-typing by PiType shown for VPipe in rows 3 through 8. Comparable presumptive annotation in VirMAP and Genome Detective (rows 3 through 8) shown as ‘-’ unless otherwise indicated.
b
Approximate length of complete viral genomes (kb), or the longest segment for segmented genomes.
c
Matches and trimming information are shown in Tables S1–, S3.
d
n/r, no results; only previously published results used for comparison.
e
Trimmed 137 bp.