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PacBio BAM C++ library
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README.md

pbbam

Build Status Documentation Status

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.

The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.

Availability

Latest pbbam can be installed via bioconda package pbbam.

Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.

Note:

This library is not intended to be used as a general-purpose BAM utility - all input & output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.

Documentation

FAQ

Help! I am getting "unsupported sequencing chemistry combination"!

pbbam validates all BAM files, and as part of this validation, it checks whether the BindingKit and SequencingKit variables in every ReadGroup of the provided BAM file are known. As part of ongoing chemistry developments, we might need to introduce new part numbers to identify novel reagents and/or SMRT Cells. You are unlikely to encounter such issues when using SMRT Link, as it has an integrated auto-updater that will periodically check and install new chemistries automatically. All PacBio tools being used without a proper SMRT Link installation will require manual intervention to download new chemistries:

cd <some persistent dir>
export SMRT_CHEMISTRY_BUNDLE_DIR="${PWD}"

wget https://raw.githubusercontent.com/PacificBiosciences/pbcore/develop/pbcore/chemistry/resources/mapping.xml -O chemistry.xml

This will cause pbbam to try to load the out-of-band chemistry.xml from SMRT_CHEMISTRY_BUNDLE_DIR and should allow you to use somewhat older software with somewhat newer BAMs. Note: this only allows pbbam's internal validation to pass, this will not automatically make other chemistry-dependent software work with newer chemistries. For instance, Arrow's backend (Unanimity) is parametrized on chemistry too, and it will fail should a completely new chemistry be introduced. See Unanimity's FAQ on how to employ SMRT_CHEMISTRY_BUNDLE_DIR to load models for new chemistries.

License

DISCLAIMER

THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

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