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.
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.
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.
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.xmlThis 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.
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