BPHL-Molecular's repositories
GentySpuds
A Nextflow workflow to seek the genotyping of Enterovirus using short-read sequencing data
flaq_sc2_clearlabs
FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for whole-genome tiled-amplicon data generated on the Clear Labs Clear Dx
flaq_sc2
FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data
Daytona_dengue
A nextflow pipeline for Dengue NGS data analysis.
flaq_sc2_meta
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)
SPARE
SPecies_Abundance_and_Reads_Extraction (SPARE)
TBx2
TB Tool Benchmarking
Pensacola
A Nextflow pipeline to analyze NGS data of Candida auris from PacBio
Daytona_combine
A combine of Daytona and Daytona_cl
Daytona
A Nextflow version of flaq_sc2
flisochar_ontlr
A Nextflow workflow to process Oxford Nanopore long-read only
Sanibel_PB
A Nextflow pipeline to analyze bacterial genome data from PacBio
Amelia
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.
Daytona_WNV
A nextflow pipeline for West Nile Virus (WNV)
flisochar_wf
A new web-deployed workflow of FLISOCHAR that processes both ONT and PacBio long reads
flaq_amr
FL-BPHL's standard bacterial assembly pipeline for taxonomic characterization and AMR detection
flisochar
Florida Bacterial Isolate Characterization
data_submission_scripts
Accessory scripts to facilitate fastq and assembly data prep for submissions to NCBI and other public repositories
Daytona_Pb
A pipeline is used to analyze SARS-CoV-2 sequencing data from PacBio equipment.
flaq_mpx
FL BPHL's Monkeypox analysis pipeline for clinical specimens
fl_cg_snp
FL BPHL's core genome SNP pipeline for the identification of clusters of closely related bacterial isolates
Daytona_cl
The Nextflow version of the Flaq_flaq_sc2_clearlabs pipeline
Enterovirus_assembler
A Nextflow pipeline for de novo assembly of Enteroviurs using fastq data