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    42 repositories

    • Juno

      Public
      Florida's BPHL Nextflow pipeline for OROV genome assembly.
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Feb 17, 2026Feb 17, 2026

    • nextstrain_orov

      Public
      Oropouche Nextstrain build for Florida local sequences
      Python
      •2•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • Jacksonville

      Public
      Rabies Analysis Pipeline
      Nextflow
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • Daytona_HAV_VPB

      Public
      A pipeline for comprehensive sequence analyses of Hepatitis A Virus (HAV) based on VP1-P2B junction region.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 30, 2026Jan 30, 2026

    • Daytona_HCV

      Public
      A pipeline for Hepatitis C virus
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

    • Daytona_HAV

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • flaq_sc2

      Public
      FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data
      Python
      •
      MIT License
      •3•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • Sanibel

      Public
      A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome
      Nextflow
      •
      Apache License 2.0
      •1•5•0•0•Updated Oct 16, 2025Oct 16, 2025

    • PhaME_m

      Public
      The debugging version of PhaME (Phylogenetic and Molecular Evolution analysis tool)
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • TB

      Public
      A directory for our extensions to CDC's varpipe platform
      Python
      •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • ReportGen

      Public
      FDOH's files for Outbreak report generation
      Jupyter Notebook
      •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025

    • KeyWest

      Public
      Nextflow pipeline for NTM analysis, mainly focus on Mycobacterium abscessus.
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Aug 22, 2025Aug 22, 2025

    • flaq_sc2_clearlabs

      Public
      FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for whole-genome tiled-amplicon data generated on the Clear Labs Clear Dx
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • SeqSender-BPHL

      Public
      The modified SeqSender specifically for Florida BPHL to upload data to NCBI
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 18, 2025Apr 18, 2025

    • .github

      Public
      MIT License
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • Sarek_Mic

      Public
      A modified version of Sarek specifically for microorganisms
      Shell
      •
      MIT License
      •0•1•0•0•Updated Nov 21, 2024Nov 21, 2024

    • flaq_sc2_meta

      Public
      FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data enriched from environmental metagenomic samples (e.g., wa…
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • Talbot

      Public
      A Nextflow pipeline for pan genome analyses including phylogenic tree. The pipeline is a upgraded version of the pipeline fl_cg_snp.
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

    • Pensacola

      Public
      A Nextflow pipeline to analyze NGS data of Candida auris from PacBio
      Perl
      •
      MIT License
      •1•1•0•2•Updated Aug 12, 2024Aug 12, 2024

    • Daytona_dengue

      Public
      A nextflow pipeline for Dengue NGS data analysis.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • SPARE

      Public
      SPecies_Abundance_and_Reads_Extraction (SPARE)
      Python
      •
      MIT License
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • TBx2

      Public
      TB Tool Benchmarking
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • Daytona_combine

      Public
      A combine of Daytona and Daytona_cl
      Nextflow
      •
      MIT License
      •2•2•0•0•Updated Mar 6, 2024Mar 6, 2024

    • Daytona

      Public
      A Nextflow version of flaq_sc2
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 6, 2024Mar 6, 2024

    • flisochar_ontlr

      Public
      A Nextflow workflow to process Oxford Nanopore long-read only
      Nextflow
      •0•0•0•0•Updated Mar 4, 2024Mar 4, 2024

    • Sanibel_PB

      Public
      A Nextflow pipeline to analyze bacterial genome data from PacBio
      Nextflow
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

    • Amelia

      Public
      A Nextflow pipeline is used to analyze Targeted NGS of Mycoplasma genitalium. The outputs include QC, amplicon statistics, SNP calling, amino acid variation det…
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • Daytona_WNV

      Public
      A nextflow pipeline for West Nile Virus (WNV)
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2023Oct 19, 2023

    • miscellaneous_scripts

      Public
      Shell
      •
      MIT License
      •1•0•0•0•Updated Oct 6, 2023Oct 6, 2023

    • flisochar_wf

      Public
      A new web-deployed workflow of FLISOCHAR that processes both ONT and PacBio long reads
      Nextflow
      •0•0•0•0•Updated Sep 14, 2023Sep 14, 2023