vaper - 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 https://github.com/DOH-JDJ0303/vaper/pull/1
• Norm ref by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/2
• added irma as option by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/3
• validation by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/5
• Irma sif by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/8
• Docker Hub -> ECR by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/9
• Dups patch by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/10
• Irma and refs by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/11
• account for samples where no sequences are classified by Sourmash by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/12
• touching up the final summary by @DOH-JDJ0303 in https://github.com/DOH-JDJ0303/vaper/pull/13

Full Changelog: https://github.com/DOH-JDJ0303/vaper/compare/%CE%B2eta...v1.0

- Nextflow
Published by DOH-JDJ0303 8 months ago

vaper - βeta

Version for beta testing.

- Nextflow
Published by DOH-JDJ0303 about 2 years ago