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PacBio bioinformatics file formats

PacBio uses the industry standard BAM format for (both aligned and unaligned) read data files. We have also formulated a BAM companion file format (bam.pbi) enabling fast access to a richer set of per-read information.

.. toctree::
   :maxdepth: 1

   Primer
   BAM
   PacBioBamIndex
   FileStructure
   FASTA
   DataSet
   RunDesignCsv

Internal file formats

.. toctree::
   :maxdepth: 1

   SubreadsBAM
   SubreadsInternalBAM

APIs available

We occasionally make changes to these file format specifications so we recommend using PacBio-authored APIs to access these file types.

Data Model XSD

For completeness, here is the PacBio data model XSD.

.. toctree::
   :maxdepth: 1

   xsd/PacBioDataModel
   xsd/PacBioAutomationConstraints
   xsd/PacBioBaseDataModel
   xsd/PacBioCollectionMetadata
   xsd/PacBioDatasets
   xsd/PacBioDeclData
   xsd/PacBioPartNumbers
   xsd/PacBioPrimaryMetrics
   xsd/PacBioReagentKit
   xsd/PacBioRightsAndRoles
   xsd/PacBioSampleInfo
   xsd/PacBioSeedingData