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@BPHL-Molecular

BPHL-Molecular

README.md

Florida BPHL's Bioinformatics pipelines and various code

  • 👋 Hi, we're a group of bioinformaticians and data analysts at Florida's Bureau of Public Health Laboratories!
  • 👩‍💻 We are active members of StaPH-B and use many of the StaPH-B resources and docker builds for our pipelines!
  • 🌱 We are currently in the process of updating all our pipelines to Nextflow - STAY TUNED!!!
  • 💞️ We are always interested to collaborate on public health bioinformatics tools and workflows for the investigation of infectious diseases.
  • 📫 How to reach us: [email protected]

Popular repositories Loading

  1. Sanibel Sanibel Public

    A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome

    Nextflow 5

  2. Daytona_combine Daytona_combine Public

    A combine of Daytona and Daytona_cl

    Nextflow 1 2

  3. Talbot 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 1

  4. data_submission_scripts data_submission_scripts Public

    Accessory scripts to facilitate fastq and assembly data prep for submissions to NCBI and other public repositories

    Python 1 1

  5. flaq_amr flaq_amr Public

    FL-BPHL's standard bacterial assembly pipeline for taxonomic characterization and AMR detection

    Python 1

  6. flaq_sc2 flaq_sc2 Public

    FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data

    Python 2

Repositories

Showing 10 of 35 repositories
  • Lyssa Public

    Rabies Analysis Pipeline

    BPHL-Molecular/Lyssa’s past year of commit activity
    0 0 0 0 Updated Nov 21, 2024
  • Sarek_Mic Public

    A modified version of Sarek specifically for microorganisms

    BPHL-Molecular/Sarek_Mic’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Nov 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., wastewater)

    BPHL-Molecular/flaq_sc2_meta’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Oct 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.

    BPHL-Molecular/Talbot’s past year of commit activity
    Nextflow 1 MIT 0 0 0 Updated Oct 1, 2024
  • PhaME_m Public

    The debugging version of PhaME (Phylogenetic and Molecular Evolution analysis tool)

    BPHL-Molecular/PhaME_m’s past year of commit activity
    0 MIT 0 0 0 Updated Sep 12, 2024
  • Sanibel Public

    A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome

    BPHL-Molecular/Sanibel’s past year of commit activity
    Nextflow 5 Apache-2.0 0 1 (1 issue needs help) 0 Updated Sep 9, 2024
  • Pensacola Public

    A Nextflow pipeline to analyze NGS data of Candida auris from PacBio

    BPHL-Molecular/Pensacola’s past year of commit activity
    Perl 0 MIT 1 0 2 Updated Aug 12, 2024
  • Daytona_dengue Public

    A nextflow pipeline for Dengue NGS data analysis.

    BPHL-Molecular/Daytona_dengue’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Aug 8, 2024
  • flaq_sc2 Public

    FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data

    BPHL-Molecular/flaq_sc2’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Aug 1, 2024
  • 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

    BPHL-Molecular/flaq_sc2_clearlabs’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Aug 1, 2024
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