Guides¶

This section contains more in-depth documents describing PacBio Data Processing, its operation and outputs as well as other related topics.

  • What is the PacBio sequencing technology?
    • PacBio protocol
    • How the PacBio sequencer output is processed?
    • sm-analysis
    • Pipeline
    • Usage
  • BAM format
    • The bam file
    • PacBio bam file
    • Aligned PacBio bam file
    • Fields
  • Summary Reports
    • Introduction
    • Description
  • Methylation Reports
    • Format
    • Format (version 2)
    • Format (version 1)
  • Raw Detections
  • Phred transformed scores
    • Definitions
    • Combining quality values
  • Using PacBio Data Processing on a cluster
    • Introduction
    • Preparation
    • Installation
    • Running
  • PacBio tools
    • SMRT-link software server tool
    • PacBio-Bioconda
  • Pbindex
    • Installing Pbindex
    • Using Pbindex from sm-analysis
  • Blasr
    • Installing Blasr
    • Using blasr from sm-analysis
  • CCS
    • Installing CCS
    • Using ccs from sm-analysis
    • Issues
  • kineticsTools
    • Installing kineticsTools
    • Using ipdSummary installed in another virtual environment
  • HTSlib
    • Installing HTSlib
  • Using Spack
    • Installing a compiler with Spack
  • Setting up Bioconda
  • Using a conda environment
  • The PacBio chemistries
    • Chemistry table
    • Chemistries in our data
  • References
  • Glossary

PacBio Data Processing

Navigation

Contents:

  • Overview
  • Quickstart for the impatient
  • Quickstart on a cluster
  • Usage
  • Guides
  • Developer’s documentation

Related Topics

  • Documentation overview
    • Previous: Using the package as a library
    • Next: What is the PacBio sequencing technology?

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