PacBio bioinformatics file formats¶
As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry standard BAM format for (both aligned and unaligned) basecall data files. We have also formulated a BAM companion file format (bam.pbi) enabling fast access to a richer set of per-read information as well as compatibility for software built around the legacy cmp.h5 format.
Legacy 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.