Repositories list

• allele-discovery

  Public
  A Snakemake workflow for discovering novel alleles with PacBio HiFi reads

  Python

  •

  MIT License

  •1•0•2•0•Updated Dec 23, 2024Dec 23, 2024

• dairy-hpai-monitoring

  Public
  Real-Time Monitoring of HPAI Detections in One or More Dairy Products in the United States

  Python

  •

  GNU General Public License v3.0

  •1•7•1•0•Updated Dec 18, 2024Dec 18, 2024

• SRA_wastewater_lineages

  Public
  Legacy repository for the SRA cryptic lineage finder featured in Suarez et al. 2025

  Python

  •1•0•6•0•Updated Dec 18, 2024Dec 18, 2024

• air_qpcr_helpeR

  Public
  Shiny apps that help work with virus qPCR data from air sample cartridges

  R

  •

  Other

  •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• Library-Rapid-Antigen-Test-Manuscript

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• Lail-et-al-2024-analysis-pipeline

  Public archive
  The version of the sequence analysis pipeline used in the preparation of Lail et al. 2024.

  Python

  •

  MIT License

  •4•0•0•0•Updated Oct 10, 2024Oct 10, 2024

• iWES-genotyper

  Public
  Python

  •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• IPD-ref-generator

  Public
  Workflow for generating useful immunological gene allele databases

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 11, 2024Jun 11, 2024

• embl-my-gbk

  Public
  Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)

  Python

  •

  MIT License

  •2•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• IPD-converter

  Public archive
  Nextflow pipeline for converting annotated, genbank-formatted novel allele sequences to Immuno Polymorphism Database format

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 10, 2024Mar 10, 2024

• air-metagenomics

  Public archive
  Analysis Pipeline for Minor and Ramuta et al. 2023: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings

  Nextflow

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jan 11, 2024Jan 11, 2024

• big-mhc-discovery

  Public
  High-throughput, reproducible pipelines for discovering and annotating novel MHC alleles in WGS data from many species

  0•0•0•0•Updated Nov 3, 2023Nov 3, 2023

• AVRL-pango-updator

  Public
  Nextflow Pipeline for Updating and Extending SARS-CoV-2 Lineage Classifications

  Nextflow

  •

  Other

  •0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

• mhc_genotyper

  Public
  MHC Class I and II genotyper for Non-Human primates with high-accuracy short reads

  Python

  •0•0•0•0•Updated Jun 16, 2023Jun 16, 2023

• snpRelate

  Public
  A Nextflow pipeline for collating SNP panel results and determining parentage

  Python

  •0•0•0•0•Updated Jun 8, 2023Jun 8, 2023

• nf-templates

  Public
  Simple NextFlow Templates for Developing your own Workflows

  Nextflow

  •1•0•0•0•Updated Mar 14, 2023Mar 14, 2023

• MHC-II-allele-discovery

  Public
  Nextflow pipeline for discovering new MHC Class II alleles in Rhesus and Cynomolgus Macaques

  Nextflow

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 27, 2023Feb 27, 2023

• Mecklenburg-et-al-2022

  Public
  Data and scripts used to confirm the discovery of a new cynomolgus macaque Hepatitis A virus

  Python

  •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

• dholab-configs

  Public
  Configuration files that, when bundled together with your nextflow workflow of choice, can configure scripts for execution on CHTC, dhogal(2), or an iMac desktop of either available architecture.

  0•0•0•0•Updated Jan 24, 2023Jan 24, 2023

• nf-iWES

  Public
  NextFlow Pipeline for genotyping immunological genes from macaque whole exome sequence data

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022

• Frequent-first-trimester-pregnancy-loss-in-rhesus-macaques-infected-with-African-lineage-Zika-virus

  Public
  We found that infection with 1X10^4 PFU ZIKV-DAK at GD30 resulted in pregnancy loss between GD 42 and GD 51 with rates of 100% for SIV+/ZIKV+ dams +ART (n=3), 50% for ZIKV+ +ART (n=3), and 100% for ZIKV+ dams -ART treatment (n=5).

  1•0•0•0•Updated Nov 3, 2022Nov 3, 2022

• E484T-visualizations

  Public
  Data visualization for manuscript on persistent infection that led to globally unique E484T mutation

  R

  •1•0•0•0•Updated Sep 29, 2022Sep 29, 2022

• prolonged-infection-suppfig1

  Public
  Pipeline for examining Intrahost Nucleotide Variants for Halfmann et al. 2022

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

• prolonged-infection-suppfig2

  Public
  Pipeline for visually comparing mutations in a persistent SARS-CoV-2 infection with the virus globally

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

• SARS-CoV-2-Spike-RBD-Analysis

  Public
  Workflow for analyzing SARS-CoV-2 spike RBD amplicon Illumina data.

  Python

  •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

• MHC_MiSeq_Genotyping_Databases

  Public
  0•0•0•0•Updated Sep 10, 2021Sep 10, 2021

• SNAILS

  Public
  Small Nucleic Acid Instrument for Long Sequences

  Python

  •0•3•2•0•Updated Aug 25, 2021Aug 25, 2021

• Shortreed-et-al-Supplemental-Code

  Public
  Supplemental Information for Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques

  Python

  •1•0•0•0•Updated Nov 15, 2019Nov 15, 2019