👋 to PacBio's GitHub space

Are you looking for great tools to analyze your HiFi data?

• aardvark - Small variant, structural variant, and tandem repeat benchmarking tool
• hificnv – Copy number variant caller and depth visualization utility
• hiphase – Small variant, structural variant, and short tandem repeat phasing tool
• isoseq – Scalable De Novo Isoform Discovery
• methbat – Battery of methylation tools
• mitorsaw - Mitochondrial variant calling and heteroplasmy detection
• owl – Microsatellite instability measures
• pangu – Star-typer for long-read PGx applications
• paraphase – Caller for highly homologous genes
• pbaa – Amplicon Analysis
• pbfusion – Fusion gene caller for Iso-Seq sequencing data.
• pbmm2 – A minimap2 frontend for PacBio native data formats
• pbsv – Structural variant calling and analysis tools
• pbtk – PacBio BAM toolkit
• sawfish – Joint structural variant and copy number variant caller for HiFi sequencing data
• skera – Kinnex HiFi read splitter
• starphase – Phase-aware pharmacogenomic diplotyper
• svpack – Filtering, comparing, and annotating structural variant
• trgt – Tandem repeat genotyping and visualization

How about complete workflows for your HiFi data?

• Amplicon Workflow
• Full-length 16S analysis - Full-length 16S sequences to report
• Metagenomic analyses
• PacBio Pipelines – Common Tasks and Workflows
• Target enrichment workflow
• HiFi somatic WDL - Call somatic variants on tumor/normal WGS data

Help pages for tools that are running on our long-read platform?

• How we demultiplex barcodes
• How we generate 5mC annotations
• How we generate HiFi reads

This list is work in progress, check out our repositories for more greatness!