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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FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binariespbbioconda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 formatsIsoSeq
IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Readspb-metagenomics-tools
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomicspb-assembly
PacBio Assembly Tool Suite: Reads in ⇨ Assembly outccs
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)pbsv
pbsv - PacBio structural variant (SV) calling and analysis toolstrgt
Tandem repeat genotyping and visualization from PacBio HiFi databarcoding
Lima - Demultiplex Barcoded PacBio SamplesHiFi-16S-workflow
Nextflow pipeline to analyze PacBio HiFi full-length 16S dataHiFi-human-WGS-WDL
HiPhase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi readssv-benchmark
Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Datapb-CpG-tools
Collection of tools for the analysis of CpG dataprimrose
Predict 5mC in PacBio HiFi readspbcore
A Python library for reading and writing PacBio® data filesbam2fastx
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.svpack
Structural variant (SV) analysis toolsFALCON-integrate
Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/BinariesFALCON_unzip
Making diploid assembly becomes common practice for genomic studyHiFiCNV
Copy number variant caller and depth visualization utility for PacBio HiFi readsPacBioFileFormats
Specifications for PacBio® native file formatspbtk
PacBio BAM toolkitpbipa
Improved Phased Assemblerapps-scripts
Miscellaneous scripts for applications of PacBio systemspbbam
PacBio BAM C++ librarypbAA
hifihla
An HLA star-calling tool for PacBio HiFi data typespbfusion
kineticsTools
Tools for detecting DNA modifications from single molecule, real-time sequencing dataANGEL
Robust Open Reading Frame prediction (ANGLE re-implementation)minorseq
Minor Variant Calling and Phasing Toolshg002-ccs
MethBat
A battery of methylation tools for PacBio HiFi readsparaphase
HiFi-based caller for highly homologous genesactc
Align subreads to ccs readspb-human-wgs-workflow-wdl
pancake
pypeFLOW
a simple lightweight workflow engine for data analysis scriptingHiFiTargetEnrichment
A repo for the Twist HiFi capture/snakemake workflowpangu
HiFi-somatic-WDL
Tumor-normal variant calling workflow using HiFi readspbcommand
PacBio common models, CLI tool contract interface and SMRT Link Service Interfacegcpp
TRexs
TRGT Repeat expansion summaryjasmine
Predict 5mC in PacBio HiFi readspb-StarPhase
A phase-aware pharmacogenomic diplotyper for PacBio datasetstrgt-denovo
De novo tandem repeat calling from PacBio HiFi datapbcopper
Core C++ library for data structures, algorithms, and utilitiesHiFi-human-assembly-WDL
CoSA
SARS-CoV-2 analysis using PacBio long readswdl-common
pbmarkdup
Mark duplicate reads from PacBio sequencing of an amplified libraryhifi-amplicon-workflow
HiFi Amplicon Workflowskera
SKERA - Deconcat PacBio readsharmony
Compute error profiles from alignmentswdl-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.recalladapters
A tool to recall adapters for PacBio datareference_genomes
pigeon
HiFi-MAG-WDL
WDL workflow for metagenomicsXiSkewAnalysis
Tools for human X-inactivation skew analysisPacBioTestData
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 pypeFLOWLove Open Source and this site? Check out how you can help us