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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FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binariespbbioconda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 datapbcore
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 readspbampliconclustering
exploratory scripts for clustering ccs amplicon datapbcommand
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