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.

Internal file formats

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.