PacBio

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89 repositories

sawfish
Public
Structural variant discovery and genotyping from mapped PacBio HiFi data
variant-calling structural-variation hifi structural-variants
Rust
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Other
•1•33•1•0•Updated Dec 13, 2024Dec 13, 2024
pbfusion
Public
Python
•3•20•2•0•Updated Dec 13, 2024Dec 13, 2024
wdl-dockerfiles
Public
Python
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BSD 3-Clause Clear License
•1•3•0•4•Updated Dec 13, 2024Dec 13, 2024
HiFi-human-WGS-WDL
Public
WDL
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BSD 3-Clause Clear License
•31•55•2•4•Updated Dec 13, 2024Dec 13, 2024
wdl-common
Public
WDL
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BSD 3-Clause Clear License
•6•4•0•1•Updated Dec 13, 2024Dec 13, 2024
pbmm2
Public
A minimap2 frontend for PacBio native data formats
Raku
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BSD 3-Clause Clear License
•29•177•2•0•Updated Dec 13, 2024Dec 13, 2024
pb-StarPhase
Public
A phase-aware pharmacogenomic diplotyper for PacBio datasets
pacbio pharmacogenomics hifi
Rust
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Other
•1•12•0•0•Updated Dec 13, 2024Dec 13, 2024
MethBat
Public
A battery of methylation tools for PacBio HiFi reads
methylation segmentation hifi pacbio-sequencing
BSD 3-Clause Clear License
•1•28•1•0•Updated Dec 12, 2024Dec 12, 2024
jasmine
Public
Predict 5mC in PacBio HiFi reads
BSD 3-Clause Clear License
•1•36•0•0•Updated Dec 12, 2024Dec 12, 2024
waffle_con
Public
DWFA consensus algorithm for pb-StarPhase
consensus pacbio pharmacogenomics hifi
Rust
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Other
•0•2•0•0•Updated Dec 5, 2024Dec 5, 2024
HiFi-human-assembly-WDL
Public
WDL
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BSD 3-Clause Clear License
•4•5•0•1•Updated Nov 26, 2024Nov 26, 2024
trgt
Public
Tandem repeat genotyping and visualization from PacBio HiFi data
Rust
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Other
•10•108•25•0•Updated Nov 25, 2024Nov 25, 2024
paraphase
Public
HiFi-based caller for highly similar paralogous genes
Python
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BSD 3-Clause Clear License
•7•36•7•0•Updated Nov 20, 2024Nov 20, 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
bioinformatics genomics data-visualization structural-variation genomics-visualization hifi structural-variants
Python
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Other
•1•27•1•0•Updated Nov 18, 2024Nov 18, 2024
HiFi-somatic-WDL
Public
Tumor-normal variant calling workflow using HiFi reads
WDL
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BSD 3-Clause Clear License
•7•12•1•1•Updated Nov 4, 2024Nov 4, 2024
vclust
Public
A method to locate variation clusters
Rust
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Other
•0•5•0•0•Updated Oct 31, 2024Oct 31, 2024
IsoSeq
Public
Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
clustering discovery pacbio rna isoforms polishing
BSD 3-Clause Clear License
•62•195•0•0•Updated Oct 29, 2024Oct 29, 2024
barcoding
Public
Lima - Demultiplex Barcoded PacBio Samples
single-molecule barcode pacbio lima demultiplexing
R
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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
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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•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
pbAA
Public
6•25•1•0•Updated Oct 28, 2024Oct 28, 2024
HiFiCNV
Public
Copy number variant caller and depth visualization utility for PacBio HiFi reads
cnv hifi pacbio-ccs
Shell
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Other
•4•39•3•0•Updated Oct 22, 2024Oct 22, 2024
trgt-denovo
Public
De novo tandem repeat calling from PacBio HiFi data
Jupyter Notebook
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Other
•1•15•2•0•Updated Oct 17, 2024Oct 17, 2024
HiPhase
Public
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
variants phasing pacbio-data hifi structural-variants short-tandem-repeats
Rust
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Other
•4•72•0•0•Updated Sep 25, 2024Sep 25, 2024
pb-metagenomics-tools
Public
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
HTML
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BSD 3-Clause Clear License
•35•179•1•0•Updated Sep 23, 2024Sep 23, 2024
pbcore
Public
A Python library for reading and writing PacBio® data files
Python
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Other
•26•39•1•1•Updated Sep 4, 2024Sep 4, 2024