PacBio Bioinformatics Tools

Contents:

• ConsensusTools
  • Circular Consensus (CCS, aka “Reads of insert”) specification
  • Amplicon Analysis
  • Running from the Command-Line
  • Arguments & Options
  • Example Files
• CorrelatedVariants
• CeleraAssembler
  • CeleraAssembler Functional Specification
• GenomicConsensus
  • Variant Caller Functional Specification
  • variants.gff File Format (Version 2.1)
  • Known Issues
  • How to install and use Quiver
  • Quiver FAQ
• kineticsTools
  • Overview
  • Algorithm
  • Inputs
  • Outputs
  • Regional m5C Detection
• pbaha
  • AHA Functional Specification
• pbalign
  • How to install and run pbalign
• pbbarcode
  • Introduction
  • Input and output
  • Dependencies
  • Barcode HDF5 File
  • Additions to the compare HDF5 (cmp.h5) File
• pbh5tools
  • Installation
  • Tool: bash5tools.py
  • Tool: cmph5tools.py
• pbreports
  • Overview
  • Setup/Install
  • Design Model
  • Report
  • Attribute
  • Table
  • PlotGroup
  • Generating Plot Images
• pbsamtools
  • PacBio SAM specification
  • Dependencies
  • Installation
  • Usage
  • Examples
  • Known Issues
  • Indices and tables