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FALCON
FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binariespbbioconda
PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.pbmm2
A minimap2 frontend for PacBio native data formatspb-metagenomics-tools
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomicsIsoSeq
IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Readsccs
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)pb-assembly
PacBio Assembly Tool Suite: Reads in โจ Assembly outtrgt
Tandem repeat genotyping and visualization from PacBio HiFi datapbsv
pbsv - PacBio structural variant (SV) calling and analysis toolsHiFi-16S-workflow
Nextflow pipeline to analyze PacBio HiFi full-length 16S dataHiPhase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi readsbarcoding
Lima - Demultiplex Barcoded PacBio SamplesHiFi-human-WGS-WDL
sv-benchmark
Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Datapb-CpG-tools
Collection of tools for the analysis of CpG datapbcore
A Python library for reading and writing PacBioยฎ data filesprimrose
Predict 5mC in PacBio HiFi readssvpack
Structural variant (SV) analysis toolsHiFiCNV
Copy number variant caller and depth visualization utility for PacBio HiFi readsbam2fastx
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.FALCON-integrate
Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/BinariesFALCON_unzip
Making diploid assembly becomes common practice for genomic studyPacBioFileFormats
Specifications for PacBioยฎ native file formatspbtk
PacBio BAM toolkitsawfish
Structural variant discovery and genotyping from mapped PacBio HiFi datapbAA
pbipa
Improved Phased Assemblerapps-scripts
Miscellaneous scripts for applications of PacBio systemspbbam
PacBio BAM C++ libraryhifihla
An HLA star-calling tool for PacBio HiFi data typesMethBat
A battery of methylation tools for PacBio HiFi readspbfusion
ANGEL
Robust Open Reading Frame prediction (ANGLE re-implementation)minorseq
Minor Variant Calling and Phasing Toolshg002-ccs
paraphase
HiFi-based caller for highly homologous genesactc
Align subreads to ccs readspb-human-wgs-workflow-wdl
trgt-denovo
De novo tandem repeat calling from PacBio HiFi dataHiFi-somatic-WDL
Tumor-normal variant calling workflow using HiFi readsHiFiTargetEnrichment
A repo for the Twist HiFi capture/snakemake workflowpancake
pypeFLOW
a simple lightweight workflow engine for data analysis scriptingpangu
pbampliconclustering
exploratory scripts for clustering ccs amplicon datapbcommand
PacBio common models, CLI tool contract interface and SMRT Link Service Interfacepb-StarPhase
A phase-aware pharmacogenomic diplotyper for PacBio datasetsTRexs
TRGT Repeat expansion summarygcpp
jasmine
Predict 5mC in PacBio HiFi readspbcopper
Core C++ library for data structures, algorithms, and utilitiesHiFi-human-assembly-WDL
CoSA
SARS-CoV-2 analysis using PacBio long readswdl-common
hifi-amplicon-workflow
HiFi Amplicon Workflowreference_genomes
pbmarkdup
Mark duplicate reads from PacBio sequencing of an amplified libraryskera
SKERA - Deconcat PacBio readswdl-dockerfiles
c3s
Generates one consensus sequence of all input CCS reads, using partial order alignmentextracthifi
Extract PacBio HiFi reads from CCS BAM filesFALCON-polish
Workflow which runs FALCON followed by polishing.HiFi-MAG-WDL
WDL workflow for metagenomicsrecalladapters
A tool to recall adapters for PacBio dataXiSkewAnalysis
Tools for human X-inactivation skew analysispigeon
PacBioTestData
Small datasets for testingzmwfilter
Filter PacBio BAM filespblaa
The project to host release binary LAA/LAAgc on biocondaFALCON-pbsmrtpipe
run.py etc using pbsmrtpipe instead of pypeFLOWharmony
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