v1.0
VAPER v1.0 was validated using 100 samples from 17 different species (see table below), sequenced using the Illumina VSP v2.0 kit. All but one sample shared >99.6% identity with published sequences. The exception being the Monkeypox virus sample, which had higher error rates in the inverted terminal repeats. As a temporary solution, a helper script has been made to mask these repeat regions in Monkeypox genomes.
| Species (subtypes) | n |
|---|---|
| Adenovirus | 7 |
| CoV-229E | 4 |
| CoV-HKU1 | 3 |
| CoV-NL63 | 3 |
| CoV-OC43 | 3 |
| Enterovirus (D68) | 1 |
| Hepatitis A virus | 1 |
| Human Metapneumovirus | 1 |
| Influenza A (H3; H1; H1N1; H3N2) | 10 |
| Influenza B | 5 |
| Measles virus | 11 |
| Monkeypox virus (IIa) | 1 |
| Mumps virus | 11 |
| Parainfluenza (3 or 4; 1 or 2; 1; 4) | 17 |
| Respiratory syncytial virus (A; B) | 4 |
| SARS-CoV-2 (BA.4.1) | 10 |
| West Nile Virus | 8 |
What's Changed
- Dev by @DOH-JDJ0303 in #1
- Norm ref by @DOH-JDJ0303 in #2
- added irma as option by @DOH-JDJ0303 in #3
- validation by @DOH-JDJ0303 in #5
- Irma sif by @DOH-JDJ0303 in #8
- Docker Hub -> ECR by @DOH-JDJ0303 in #9
- Dups patch by @DOH-JDJ0303 in #10
- Irma and refs by @DOH-JDJ0303 in #11
- account for samples where no sequences are classified by Sourmash by @DOH-JDJ0303 in #12
- touching up the final summary by @DOH-JDJ0303 in #13
Full Changelog: βeta...v1.0
Contributors
DOH-JDJ0303