Repositories list

• phipseq

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• rumina

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

  Rust

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• MPV_genomics

  Public
  HTML

  •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• revica-strm

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

  Nextflow

  •2•0•0•0•Updated Feb 21, 2025Feb 21, 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 outbreaks to investigate the immunity debt hypothesis".

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• RAVA_Pipeline

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• revica

  Public
  A reference-based viral consensus genome assembly pipeline

  Nextflow

  •3•7•1•1•Updated Jan 22, 2025Jan 22, 2025

• vadr_annotator

  Public
  Perl

  •

  MIT License

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• vadr-models-hpiv

  Public
  Human parainfluenza virus (HPIV) VADR models

  JavaScript

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• pneumovirus_misassemblies

  Public
  0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• tp_coinfection

  Public
  R

  •1•0•0•0•Updated Nov 16, 2024Nov 16, 2024

• vadr-models-hmpv

  Public
  Human metapneumovirus (HMPV) VADR models

  JavaScript

  •0•0•1•0•Updated Nov 13, 2024Nov 13, 2024

• nf_mpxv_f13l

  Public
  A nextflow pipeline for MPXV consensus genome assembly and F13L variants calling

  Nextflow

  •1•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• rad_assembler

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

  Nextflow

  •

  MIT License

  •1•0•3•0•Updated Sep 9, 2024Sep 9, 2024

• mpxv_wgs

  Public
  A nextflow pipeline for monkeypox virus consensus genome assembly and variants calling

  Nextflow

  •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

• rsv_ampseq

  Public
  Nextflow pipeline for genome assembly and variants calling of human respiratory syncytial virus amplicon sequencing

  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

• Yin_CHIKV_fidelity_supp

  Public
  Supplemental information for Figures 4 and 5 of Mutations in Chikungunya Virus nsP4 Decrease Sensitivity to the Broad-Spectrum Antiviral 4′-Fluorouridine.

  HTML

  •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

• vadr-models-hsv

  Public
  Human alphaherpesvirus 1 and 2 (HSV-1, HSV-2) VADR models

  Batchfile

  •1•0•0•0•Updated Jul 23, 2024Jul 23, 2024

• HRV_epidemiology

  Public
  HTML

  •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• TPRK-Pipeline

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• sars-cov-2_mouse_model_supp

  Public
  Data tables and figure generation scripts

  HTML

  •0•0•0•0•Updated May 10, 2024May 10, 2024

• Tpallidum_WGS_Pipeline

  Public
  Nextflow

  •0•1•0•0•Updated Apr 25, 2024Apr 25, 2024

• lava

  Public archive
  LAVA: Longitudinal Analysis of Viral Alleles

  Python

  •

  GNU General Public License v3.0

  •7•3•0•0•Updated Apr 19, 2024Apr 19, 2024

• tprk

  Public archive
  R

  •

  MIT License

  •4•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• Tpallidum_WGS

  Public archive
  assembly and annotation of Treponema pallidum genomes

  Nextflow

  •3•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• greninger-lab.github.io

  Public
  Astro

  •

  MIT License

  •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

• viralrecon

  Public
  Assembly and intrahost/low-frequency variant calling for viral samples - Greninger Lab

  Nextflow

  •

  MIT License

  •116•0•0•0•Updated Jan 16, 2024Jan 16, 2024

• covid_swift_pipeline

  Public
  Nextflow

  •

  MIT License

  •7•4•0•0•Updated Jan 6, 2024Jan 6, 2024

• assay-validation

  Public
  0•0•0•0•Updated Jan 2, 2024Jan 2, 2024

• cfdna_hunter

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Dec 21, 2023Dec 21, 2023