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    86 repositories

    • HiFi-somatic-WDL

      Public
      Tumor-normal variant calling workflow using HiFi reads
      WDL
      •
      BSD 3-Clause Clear License
      •6•12•0•1•Updated Oct 1, 2024Oct 1, 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•67•0•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
      •34•168•2•0•Updated Sep 23, 2024Sep 23, 2024

    • IsoSeq

      Public
      Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
      clusteringdiscoverypacbiornaisoformspolishing
      BSD 3-Clause Clear License
      •61•190•0•1•Updated Sep 17, 2024Sep 17, 2024

    • trgt

      Public
      Tandem repeat genotyping and visualization from PacBio HiFi data
      Rust
      •
      Other
      •7•103•19•0•Updated Sep 17, 2024Sep 17, 2024

    • sawfish

      Public
      Structural variant discovery and genotyping from mapped PacBio HiFi data
      variant-callingstructural-variationhifistructural-variants
      Rust
      •
      Other
      •1•23•1•0•Updated Sep 13, 2024Sep 13, 2024

    • pb-StarPhase

      Public
      A phase-aware pharmacogenomic diplotyper for PacBio datasets
      pacbiopharmacogenomicshifi
      BSD 3-Clause Clear License
      •1•10•0•0•Updated Sep 10, 2024Sep 10, 2024

    • HiFi-human-WGS-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •26•50•3•1•Updated Sep 5, 2024Sep 5, 2024

    • wdl-common

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •5•4•0•2•Updated Sep 4, 2024Sep 4, 2024

    • wdl-dockerfiles

      Public
      Python
      •
      BSD 3-Clause Clear License
      •0•3•0•4•Updated Sep 4, 2024Sep 4, 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

    • trgt-denovo

      Public
      De novo tandem repeat calling from PacBio HiFi data
      Jupyter Notebook
      •
      Other
      •1•12•0•0•Updated Aug 30, 2024Aug 30, 2024

    • MethBat

      Public
      A battery of methylation tools for PacBio HiFi reads
      methylationsegmentationhifipacbio-sequencing
      BSD 3-Clause Clear License
      •0•26•0•0•Updated Aug 27, 2024Aug 27, 2024

    • HiFi-MAG-WDL

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

    • HiFi-human-assembly-WDL

      Public
      WDL
      •
      BSD 3-Clause Clear License
      •2•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

    • pbbioconda

      Public
      PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
      BSD 3-Clause Clear License
      •44•249•9•0•Updated Jun 25, 2024Jun 25, 2024

    • pbmm2

      Public
      A minimap2 frontend for PacBio native data formats
      Perl
      •
      BSD 3-Clause Clear License
      •27•170•2•0•Updated Jun 11, 2024Jun 11, 2024

    • paraphase

      Public
      HiFi-based caller for highly similar paralogous genes
      Python
      •
      BSD 3-Clause Clear License
      •4•29•5•0•Updated May 21, 2024May 21, 2024

    • HiFiTargetEnrichment

      Public
      A repo for the Twist HiFi capture/snakemake workflow
      Python
      •
      BSD 3-Clause Clear License
      •1•11•2•2•Updated May 15, 2024May 15, 2024

    • pbfusion

      Public
      Python
      •2•19•2•0•Updated Apr 17, 2024Apr 17, 2024

    • pbAA

      Public
      5•24•1•0•Updated Apr 16, 2024Apr 16, 2024

    • hifihla

      Public
      An HLA star-calling tool for PacBio HiFi data types
      sequencingdnapacbioimmunologyhlaimgthla-typinghifi
      BSD 3-Clause Clear License
      •2•20•1•0•Updated Apr 11, 2024Apr 11, 2024

    • pangu

      Public
      Python
      •
      BSD 3-Clause Clear License
      •3•10•0•0•Updated Apr 9, 2024Apr 9, 2024

    • HiFiCNV

      Public
      Copy number variant caller and depth visualization utility for PacBio HiFi reads
      cnvhifipacbio-ccs
      Shell
      •
      BSD 3-Clause Clear License
      •4•35•2•0•Updated Mar 27, 2024Mar 27, 2024

    • .github

      Public
      0•1•0•0•Updated Mar 26, 2024Mar 26, 2024

    • ccs

      Public
      CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
      machine-learningbioinformaticsconsensuspacbiovariant-callingccs
      BSD 3-Clause Clear License
      •30•115•0•0•Updated Mar 18, 2024Mar 18, 2024

    • pb-CpG-tools

      Public
      Collection of tools for the analysis of CpG data
      BSD 3-Clause Clear License
      •6•70•8•0•Updated Feb 22, 2024Feb 22, 2024

    • barcoding

      Public
      Lima - Demultiplex Barcoded PacBio Samples
      single-moleculebarcodepacbiolimademultiplexing
      R
      •
      BSD 3-Clause Clear License
      •23•65•0•0•Updated Dec 18, 2023Dec 18, 2023

    • HiFi-16S-workflow

      Public
      Nextflow pipeline to analyze PacBio HiFi full-length 16S data
      Nextflow
      •
      BSD 3-Clause Clear License
      •15•61•5•0•Updated Dec 14, 2023Dec 14, 2023