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    35 repositories

    • 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
      •1•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • flaq_sc2

      Public
      FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data
      Python
      •
      MIT License
      •2•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • Lyssa

      Public
      Rabies Analysis Pipeline
      0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • Sarek_Mic

      Public
      A modified version of Sarek specifically for microorganisms
      Shell
      •
      MIT License
      •0•0•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., wastewater)
      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

    • PhaME_m

      Public
      The debugging version of PhaME (Phylogenetic and Molecular Evolution analysis tool)
      MIT License
      •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • Sanibel

      Public
      A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome
      Nextflow
      •
      Apache License 2.0
      •0•5•1•0•Updated Sep 9, 2024Sep 9, 2024

    • Pensacola

      Public
      A Nextflow pipeline to analyze NGS data of Candida auris from PacBio
      Perl
      •
      MIT License
      •1•0•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

    • GentySpuds

      Public
      A Nextflow workflow to seek the genotyping of Enterovirus using short-read sequencing data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 18, 2024Jul 18, 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•1•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 detection, etc.
      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

    • flaq_amr

      Public
      FL-BPHL's standard bacterial assembly pipeline for taxonomic characterization and AMR detection
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • flisochar

      Public
      Florida Bacterial Isolate Characterization
      Python
      •0•0•0•0•Updated Jul 25, 2023Jul 25, 2023

    • .github

      Public
      MIT License
      •0•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • data_submission_scripts

      Public
      Accessory scripts to facilitate fastq and assembly data prep for submissions to NCBI and other public repositories
      Python
      •
      MIT License
      •1•1•0•0•Updated Jun 20, 2023Jun 20, 2023

    • wrapper_Nextstrain_SARSCov2

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Mar 16, 2023Mar 16, 2023

    • Daytona_Pb

      Public
      A pipeline is used to analyze SARS-CoV-2 sequencing data from PacBio equipment.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • sc2_review_submission

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • flaq_mpx

      Public
      FL BPHL's Monkeypox analysis pipeline for clinical specimens
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • fl_cg_snp

      Public
      FL BPHL's core genome SNP pipeline for the identification of clusters of closely related bacterial isolates
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 13, 2023Feb 13, 2023