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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FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binariespbbioconda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 ⇨ 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 PacBio® data filesprimrose
Predict 5mC in PacBio HiFi readssvpack
Structural variant (SV) analysis toolsbam2fastx
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 PacBio® 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
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
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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