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    89 repositories

    • HiFi-SVTopo

      Public
      Complex structural variant visualization for HiFi sequencing data
      bioinformaticsgenomicsdata-visualizationstructural-variationgenomics-visualizationhifistructural-variants
      Python
      •
      Other
      •1•26•2•0•Updated Nov 17, 2024Nov 17, 2024

    • HiFi-human-WGS-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •31•52•2•1•Updated Nov 16, 2024Nov 16, 2024

    • wdl-common

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •6•4•0•1•Updated Nov 16, 2024Nov 16, 2024

    • paraphase

      Public
      HiFi-based caller for highly similar paralogous genes
      Python
      •
      BSD 3-Clause Clear License
      •5•36•6•0•Updated Nov 11, 2024Nov 11, 2024

    • wdl-dockerfiles

      Public
      Python
      •
      BSD 3-Clause Clear License
      •1•3•0•3•Updated Nov 11, 2024Nov 11, 2024

    • HiFi-somatic-WDL

      Public
      Tumor-normal variant calling workflow using HiFi reads
      WDL
      •
      BSD 3-Clause Clear License
      •7•12•0•1•Updated Nov 4, 2024Nov 4, 2024

    • vclust

      Public
      A method to locate variation clusters
      Rust
      •
      Other
      •0•5•0•0•Updated Oct 31, 2024Oct 31, 2024

    • jasmine

      Public
      Predict 5mC in PacBio HiFi reads
      BSD 3-Clause Clear License
      •1•32•0•0•Updated Oct 30, 2024Oct 30, 2024

    • pbmm2

      Public
      A minimap2 frontend for PacBio native data formats
      Raku
      •
      BSD 3-Clause Clear License
      •27•176•2•0•Updated Oct 29, 2024Oct 29, 2024

    • IsoSeq

      Public
      Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
      clusteringdiscoverypacbiornaisoformspolishing
      BSD 3-Clause Clear License
      •62•192•0•0•Updated Oct 29, 2024Oct 29, 2024

    • barcoding

      Public
      Lima - Demultiplex Barcoded PacBio Samples
      single-moleculebarcodepacbiolimademultiplexing
      R
      •
      BSD 3-Clause Clear License
      •23•65•0•0•Updated Oct 29, 2024Oct 29, 2024

    • pbsv

      Public
      pbsv - PacBio structural variant (SV) calling and analysis tools
      Python
      •
      BSD 3-Clause Clear License
      •23•130•0•0•Updated Oct 29, 2024Oct 29, 2024

    • skera

      Public
      SKERA - Deconcat PacBio reads
      BSD 3-Clause Clear License
      •2•6•0•0•Updated Oct 29, 2024Oct 29, 2024

    • pbmarkdup

      Public
      Mark duplicate reads from PacBio sequencing of an amplified library
      BSD 3-Clause Clear License
      •4•10•0•0•Updated Oct 29, 2024Oct 29, 2024

    • pbtk

      Public
      PacBio BAM toolkit
      BSD 3-Clause Clear License
      •2•39•0•0•Updated Oct 29, 2024Oct 29, 2024

    • pigeon

      Public
      BSD 3-Clause Clear License
      •0•4•0•0•Updated Oct 29, 2024Oct 29, 2024

    • pb-StarPhase

      Public
      A phase-aware pharmacogenomic diplotyper for PacBio datasets
      pacbiopharmacogenomicshifi
      Rust
      •
      Other
      •1•10•0•0•Updated Oct 28, 2024Oct 28, 2024

    • pbAA

      Public
      6•25•1•0•Updated Oct 28, 2024Oct 28, 2024

    • sawfish

      Public
      Structural variant discovery and genotyping from mapped PacBio HiFi data
      variant-callingstructural-variationhifistructural-variants
      Rust
      •
      Other
      •1•30•0•0•Updated Oct 23, 2024Oct 23, 2024

    • waffle_con

      Public
      DWFA consensus algorithm for pb-StarPhase
      consensuspacbiopharmacogenomicshifi
      Rust
      •
      Other
      •0•2•0•0•Updated Oct 23, 2024Oct 23, 2024

    • HiFiCNV

      Public
      Copy number variant caller and depth visualization utility for PacBio HiFi reads
      cnvhifipacbio-ccs
      Shell
      •
      Other
      •4•38•4•0•Updated Oct 22, 2024Oct 22, 2024

    • trgt-denovo

      Public
      De novo tandem repeat calling from PacBio HiFi data
      Jupyter Notebook
      •
      Other
      •1•14•0•0•Updated Oct 17, 2024Oct 17, 2024

    • HiPhase

      Public
      Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
      variantsphasingpacbio-datahifistructural-variantsshort-tandem-repeats
      Rust
      •
      Other
      •4•70•1•0•Updated Sep 25, 2024Sep 25, 2024

    • pb-metagenomics-tools

      Public
      Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
      HTML
      •
      BSD 3-Clause Clear License
      •36•178•1•0•Updated Sep 23, 2024Sep 23, 2024

    • trgt

      Public
      Tandem repeat genotyping and visualization from PacBio HiFi data
      Rust
      •
      Other
      •8•106•20•0•Updated Sep 17, 2024Sep 17, 2024

    • pbcore

      Public
      A Python library for reading and writing PacBio® data files
      Python
      •
      Other
      •26•39•1•1•Updated Sep 4, 2024Sep 4, 2024

    • MethBat

      Public
      A battery of methylation tools for PacBio HiFi reads
      methylationsegmentationhifipacbio-sequencing
      BSD 3-Clause Clear License
      •1•28•0•0•Updated Aug 27, 2024Aug 27, 2024

    • HiFi-MAG-WDL

      Public
      WDL workflow for metagenomics
      WDL
      •
      BSD 3-Clause Clear License
      •1•3•0•0•Updated Jul 3, 2024Jul 3, 2024

    • HiFi-human-assembly-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •3•5•0•1•Updated Jul 3, 2024Jul 3, 2024

    • svpack

      Public
      Structural variant (SV) analysis tools
      Python
      •
      BSD 3-Clause Clear License
      •3•36•0•0•Updated Jul 1, 2024Jul 1, 2024