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    90 repositories

    • HiFi-somatic-WDL

      Public
      Tumor-normal variant calling workflow using HiFi reads
      WDL
      •
      BSD 3-Clause Clear License
      •8•15•1•1•Updated Feb 21, 2025Feb 21, 2025

    • HiFi-16S-workflow

      Public
      Nextflow pipeline to analyze PacBio HiFi full-length 16S data
      Nextflow
      •
      BSD 3-Clause Clear License
      •18•66•6•0•Updated Feb 21, 2025Feb 21, 2025

    • HiFi-human-WGS-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •36•55•3•4•Updated Feb 20, 2025Feb 20, 2025

    • pbcore

      Public
      A Python library for reading and writing PacBio® data files
      Python
      •
      Other
      •27•40•2•2•Updated Feb 20, 2025Feb 20, 2025

    • wdl-common

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •10•4•0•1•Updated Feb 18, 2025Feb 18, 2025

    • pb-StarPhase

      Public
      A phase-aware pharmacogenomic diplotyper for PacBio datasets
      pacbiopharmacogenomicshifi
      Rust
      •
      Other
      •1•12•1•0•Updated Feb 14, 2025Feb 14, 2025

    • pb-metagenomics-tools

      Public
      Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
      HTML
      •
      BSD 3-Clause Clear License
      •35•182•2•0•Updated Feb 12, 2025Feb 12, 2025

    • wdl-dockerfiles

      Public
      Python
      •
      BSD 3-Clause Clear License
      •1•3•0•3•Updated Feb 11, 2025Feb 11, 2025

    • paraphase

      Public
      HiFi-based caller for highly similar paralogous genes
      Python
      •
      BSD 3-Clause Clear License
      •7•36•8•0•Updated Feb 10, 2025Feb 10, 2025

    • trgt

      Public
      Tandem repeat genotyping and visualization from PacBio HiFi data
      Rust
      •
      Other
      •10•114•29•0•Updated Feb 7, 2025Feb 7, 2025

    • trgt-denovo

      Public
      De novo tandem repeat calling from PacBio HiFi data
      Jupyter Notebook
      •
      Other
      •1•15•0•0•Updated Feb 4, 2025Feb 4, 2025

    • pb-CpG-tools

      Public
      Collection of tools for the analysis of CpG data
      Rust
      •
      Other
      •6•77•3•0•Updated Feb 4, 2025Feb 4, 2025

    • pbbioconda

      Public
      PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
      BSD 3-Clause Clear License
      •45•261•18•0•Updated Feb 4, 2025Feb 4, 2025

    • minimap2

      Public
      A versatile pairwise aligner for genomic and spliced nucleotide sequences
      C
      •
      Other
      •425•8•0•0•Updated Jan 24, 2025Jan 24, 2025

    • waffle_graph

      Public
      Rust
      •
      Other
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • sawfish

      Public
      Structural variant discovery and genotyping from mapped PacBio HiFi data
      variant-callingstructural-variationhifistructural-variants
      Rust
      •
      Other
      •1•40•1•0•Updated Jan 16, 2025Jan 16, 2025

    • pbfusion

      Public
      Python
      •3•20•2•0•Updated Dec 13, 2024Dec 13, 2024

    • pbmm2

      Public
      A minimap2 frontend for PacBio native data formats
      Raku
      •
      BSD 3-Clause Clear License
      •31•181•2•0•Updated Dec 13, 2024Dec 13, 2024

    • pb-benchmarks

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • MethBat

      Public
      A battery of methylation tools for PacBio HiFi reads
      methylationsegmentationhifipacbio-sequencing
      BSD 3-Clause Clear License
      •1•31•0•0•Updated Dec 12, 2024Dec 12, 2024

    • waffle_con

      Public
      DWFA consensus algorithm for pb-StarPhase
      consensuspacbiopharmacogenomicshifi
      Rust
      •
      Other
      •0•2•0•0•Updated Dec 5, 2024Dec 5, 2024

    • HiFi-human-assembly-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •4•5•0•1•Updated Nov 26, 2024Nov 26, 2024

    • PacBioFileFormats

      Public
      Specifications for PacBio® native file formats
      Python
      •17•30•0•0•Updated Nov 19, 2024Nov 19, 2024

    • HiFi-SVTopo

      Public
      Complex structural variant visualization for HiFi sequencing data
      bioinformaticsgenomicsdata-visualizationstructural-variationgenomics-visualizationhifistructural-variants
      Python
      •
      Other
      •1•27•4•0•Updated Nov 18, 2024Nov 18, 2024

    • vclust

      Public
      A method to locate variation clusters
      Rust
      •
      Other
      •0•6•0•0•Updated Oct 31, 2024Oct 31, 2024

    • IsoSeq

      Public
      Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
      clusteringdiscoverypacbiornaisoformspolishing
      BSD 3-Clause Clear License
      •63•203•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
      •24•132•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•11•0•0•Updated Oct 29, 2024Oct 29, 2024