Repositories list

• revica

  Public
  A reference-based viral consensus genome assembly pipeline

  Nextflow

  •5•8•1•1•Updated Mar 25, 2026Mar 25, 2026

• vadr-models-hrv

  Public
  Human rhinovirus (HRV) VADR model libraries

  JavaScript

  •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• revica-strm

  Public
  An accelerated pipeline for reference-based assembly of viral genomes from capture and metagenomic short read sequencing data

  Nextflow

  •2•1•1•0•Updated Mar 4, 2026Mar 4, 2026

• vadr-models-ev

  Public
  Human enterovirus (EV) VADR model libraries

  JavaScript

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• covid_swift_pipeline

  Public
  Nextflow

  •

  MIT License

  •7•4•0•0•Updated Feb 23, 2026Feb 23, 2026

• tprk-argentina

  Public
  Python

  •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

• vadr-vscan-aglab

  Public
  Use VADR v-scan to annotate HCoV, HMPV, HPIV, MeV, MuV or RuV sequences.

  Shell

  •0•3•0•0•Updated Jan 28, 2026Jan 28, 2026

• rumina

  Public
  A high-throughput error correction pipeline for NGS data using Unique Molecular Identifiers (UMIs).

  Rust

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Jan 22, 2026Jan 22, 2026

• rumina_paper

  Public
  HTML

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

• anellovirus_in_skno1_paper

  Public
  Shell

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• tpallidum-variant-calling

  Public
  Nextflow

  •

  MIT License

  •0•2•0•0•Updated Dec 9, 2025Dec 9, 2025

• RAVA_Pipeline

  Public
  RAVA (Reference-based Analysis of Viral Alleles) is a Nextflow-based pipeline for non-longitudinal viral NGS data that generates interactive browser visualizati…

  virussnvngs-pipeline

  virussnvngs-pipeline

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 8, 2025Dec 8, 2025

• MPXV_MSD_validation_paper

  Public
  Data and figure generation for the MPXV MSD validation manuscript

  R

  •0•0•0•0•Updated Dec 2, 2025Dec 2, 2025

• rad_assembler

  Public
  Nextflow pipeline for Reference Assisted De novo assembling whole genome shotgun sequenced viruses.

  Nextflow

  •

  MIT License

  •1•0•3•0•Updated Nov 6, 2025Nov 6, 2025

• rsv_neut_paper

  Public
  Data and analysis used for the manuscript "Clinical validation of an RSV neutralization assay and analysis of cross-sectional sera associated with 2021–2023 RSV…

  0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

• positional_nuc_profiler

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

• phipseq

  Public
  PhIP-Seq repository containing scripts and metadata files for the paper 'Immunization with full-length TprC variants induces a broad response to surface-exposed…

  R

  •

  MIT License

  •0•0•0•0•Updated Oct 1, 2025Oct 1, 2025

• Orthorubulavirus_HPIV

  Public
  HTML

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• MPV_genomics

  Public
  HTML

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• pneumovirus_misassemblies

  Public
  0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• HRV_Epidemiology

  Public
  HTML

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• HRV_Within-host

  Public
  Files and pipelines used to generate figures

  PostScript

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• RSV-WA-2022

  Public
  0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• vadr-respiratory-virus

  Public
  0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• oropharyngeal_resistome

  Public
  Oropharyngeal resistome nextflow pipeline

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• vadr-models-hav

  Public
  Hepatitis A virus (HAV) VADR model library

  JavaScript

  •0•1•0•0•Updated Sep 2, 2025Sep 2, 2025

• vadr-vscan-ncbi-resp

  Public
  Use VADR v-scan to annotate Sars-CoV-2, flu, and RSV sequences.

  Shell

  •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• hadv_phf_typing_db

  Public
  Human adenovirus typing database

  JavaScript

  •0•0•1•0•Updated Jul 24, 2025Jul 24, 2025

• vadr-models-mev

  Public
  Measles (MeV) VADR models

  JavaScript

  •0•1•0•0•Updated Jul 7, 2025Jul 7, 2025

• vadr-models-muv

  Public
  Mumps (MuV) VADR models

  JavaScript

  •0•0•0•1•Updated Jul 7, 2025Jul 7, 2025