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Tools & APIs

Conversion Tools

The SMRT® Pipe software includes several tools for file conversion and access. They generate some of the outputs from the analysis pipeline.

• HDF5 to FASTA A python script to convert PacBio HDF5 files into FASTA format
• HDF5 to SAM/BAM A python script to convert PacBio HDF5 files into SAM/BAM format
• GFF to BED A python script to convert variants GFF files into BED format.
• GFF to VCF A python script to convert variants GFF files into VCF format.

Web Service APIs

To integrate with the PacBio instrument and secondary analysis software, take a look at the web service API docs.

• Instrument Web Services, a RESTful API to facilitate integration with LIMS and your own data analysis pipelines.
• Secondary Analysis Web Services, a RESTful API to manage all aspects of secondary data analysis within a production environment.

File APIs

To access PacBio data files, our software engineers and bioinformaticians wrote these APIs. They are available as separate (and small!) downloads like any other community-contributed code. We encourage you to share conversion tools or APIs that you have developed and think may be useful to others.

• HDF5 Base, Trace, Pulse and Circular Consensus File Java API A Java API to read base, trace, pulse and circular consensus sequencing basecall files.
• HDF5 R API An R API to read HDF5 base files produced by the instrument and by SMRT Analysis.