index.rst

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.

Primer BAM PacBioBamIndex FileStructure FASTA DataSet RunDesignCsv

Internal file formats

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.

• C++: pbbam
• Python: pbcore

Data Model XSD

For completeness, here is the PacBio data model XSD.

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