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.

• Brief primer and lexicon for PacBio SMRT sequencing
• PacBio BAM format specification
• PacBio BAM index file (bam.pbi) format
• Revio & Vega file structure
• FASTA file format
• DataSet format specification

Internal file formats

• BAM format additions for PacBio-subreads
• BAM format additions for PacBio-internal analysis

Data Model XSD

For completeness, here is the PacBio data model XSD.

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