Pinned Repositories
data_submission_scripts
Accessory scripts to facilitate fastq and assembly data prep for submissions to NCBI and other public repositories
fl_cg_snp
FL BPHL's core genome SNP pipeline for the identification of clusters of closely related bacterial isolates
flisochar
Florida Bacterial Isolate Characterization
flisochar_wf
A new web-deployed workflow of FLISOCHAR that processes both ONT and PacBio long reads
GentySpuds
A Nextflow workflow to seek the genotyping of Enterovirus using short-read sequencing data
miscellaneous_scripts
Nextflow_cat_nextseq_fastqs_BSupload
The Nextflow version of cat_nextseq_fastqs_BSupload.py
PacBio_standalone_tools
Sanibel
A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome
Talbot
A Nextflow pipeline for pang genome analyses including phylogenic tree. The pipeline is a upgraded version of the pipeline fl_cg_snp.
BPHL-Molecular's Repositories
BPHL-Molecular/Sanibel
A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome
BPHL-Molecular/data_submission_scripts
Accessory scripts to facilitate fastq and assembly data prep for submissions to NCBI and other public repositories
BPHL-Molecular/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.
BPHL-Molecular/Daytona_combine
A combine of Daytona and Daytona_cl
BPHL-Molecular/Daytona_dengue
A nextflow pipeline for Dengue NGS data analysis.
BPHL-Molecular/fl_cg_snp
FL BPHL's core genome SNP pipeline for the identification of clusters of closely related bacterial isolates
BPHL-Molecular/flisochar
Florida Bacterial Isolate Characterization
BPHL-Molecular/flisochar_ontlr
A Nextflow workflow to process Oxford Nanopore long-read only
BPHL-Molecular/flisochar_wf
A new web-deployed workflow of FLISOCHAR that processes both ONT and PacBio long reads
BPHL-Molecular/GentySpuds
A Nextflow workflow to seek the genotyping of Enterovirus using short-read sequencing data
BPHL-Molecular/miscellaneous_scripts
BPHL-Molecular/PacBio_standalone_tools
BPHL-Molecular/Pensacola
A Nextflow pipeline to analyze NGS data of Candida auris from PacBio
BPHL-Molecular/Sanibel_PB
A Nextflow pipeline to analyze bacterial genome data from PacBio
BPHL-Molecular/.github
BPHL-Molecular/Daytona
A Nextflow version of flaq_sc2
BPHL-Molecular/Daytona_cl
The Nextflow version of the Flaq_flaq_sc2_clearlabs pipeline
BPHL-Molecular/Daytona_Pb
A pipeline is used to analyze SARS-CoV-2 sequencing data from PacBio equipment.
BPHL-Molecular/Daytona_WNV
A nextflow pipeline for West Nile Virus (WNV)
BPHL-Molecular/Enterovirus_assembler
A Nextflow pipeline for de novo assembly of Enteroviurs using fastq data
BPHL-Molecular/flaq_amr
FL-BPHL's standard bacterial assembly pipeline for taxonomic characterization and AMR detection
BPHL-Molecular/flaq_mpx
FL BPHL's Monkeypox analysis pipeline for clinical specimens
BPHL-Molecular/flaq_sc2
FL BPHL's SARS-CoV-2 (SC2) analysis pipeline for Illumina paired-end, whole-genome tiled-amplicon data
BPHL-Molecular/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
BPHL-Molecular/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)
BPHL-Molecular/PhaME_m
The debugging version of PhaME (Phylogenetic and Molecular Evolution analysis tool)
BPHL-Molecular/sc2_review_submission
BPHL-Molecular/SPARE
SPecies_Abundance_and_Reads_Extraction (SPARE)
BPHL-Molecular/TBx2
TB Tool Benchmarking
BPHL-Molecular/wrapper_Nextstrain_SARSCov2