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.

C++: pbbam
Python: pbcore

Data Model XSD¶

For completeness, here is the PacBio data model XSD.