PacBio Secondary Analysis Tools on Bioconda
PacBio® tools distributed via Bioconda are: pre-release versions, not necessarily ISO compliant, intended for Research Use Only and not for use in diagnostic procedures, intended only for command-line users, and possibly newer than the currently available SMRT® Analysis builds. While efforts have been made to ensure that releases on Bioconda live up to the quality that PacBio strives for, we make no warranty regarding any Bioconda release.
As PacBio tools distributed via Bioconda are not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientist or PacBio Customer Service for assistance with any Bioconda release. We instead provide an issue tracker for you to report issues to us at: https://github.com/PacificBiosciences/pbbioconda. We make no warranty that any such issue will be addressed, to any extent or within any time frame.
Official tech support is only provided for official and stable SMRT Link releases provided by PacBio.
No support via mail to developers.
For issues with the installation of conda or adding the bioconda channel, please refer to the official bioconda website.
For issues with installed PacBio binaries through bioconda, please create a new issue! Our developers will triage your problems internally and reply as soon as possible.
If required to share a file for easier troubleshooting, please use PacBio's file drop-off. You do not need a "request code". Enter your name and mail to receive a drop-off link. Once received via mail, you will be forwarded to your personal drop-off page, where you will be asked to enter a PacBio recipient. Please enter firstname.lastname@example.org and proceed to upload your files. More info about file transfer security.
Information how to install
conda and add the
bioconda channel is
available on https://bioconda.github.io/. Please verify that you have set up conda channel priorities according to set up conda channels.
Packages can be installed using following command:
> conda install -c bioconda package_name
Packages can be updated with:
> conda update package_name
In general, because conda only performs the smallest set of updates in order to satisfy the dependency graph, it is strongly advised to always update the environment as a whole afterwards:
> conda update --all
In order to avoid stale dependencies in the dependency graph.
- Python packages require version 2.7; Python 3 is currently not supported! You cannot install PacBio packages alongside python 3-only packages in the same environment! In order to use python 3-only packages, create a separate conda env.
- BAM refers to the PacBio BAM format that includes additional per-record or per-ZMW information
- Packages might conflict with other bioconda packages not maintained by PacBio
|bam2fastx||Y||Y||Convert and split BAM files into fasta.gz and fastq.gz|
|bax2bam||Y||Y||Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to BAM|
|blasr||Y||Y||The long read aligner|
|extracthifi||Y||-||Extract HiFi reads from full CCS output|
|genomicconsensus||Y||Y||Polish genome assemblies. Attention: deprecated and replaced by
|isoseq3||Y||-||Scalable de novo isoform discovery (Release Notes)|
|lima||Y||-||Demultiplex barcoded samples (Release Notes)|
|minorseq||Y||-||Minor Variant Calling and Phasing Tools|
|pbaa||Y||Y||HiFi specific Amplicon Analysis|
|pbalign||Y||Y||Python wrapper for BLASR and associated tools|
|pbbam||Y||Y||BAM C++ library (Release Notes)|
|pbccs||Y||-||Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads) (Release Notes)|
|pbcommand||Y||Y||Common models, CLI tool contract and SMRT Link service interface|
|pbcopper||Y||Y||Core C++ library for data structures, algorithms, and utilities (Release Notes)|
|pbcore||Y||Y||Python library for reading and writing data files|
|pbcoretools||Y||Y||CLI tools and add-ons for PacBio's core APIs (incl
|pbgcpp||Y||-||C++ port of assembly polisher. Replaces variantCaller/arrow (Release Notes)|
|pbipa||Y||-||Construct very contiguous, high quality de novo genome assemblies using the IPA HiFi assembler. (Release Notes)|
|pblaa||Y||-||Long amplicon analysis|
|pbmarkdup||Y||-||Mark duplicate reads from PacBio sequencing of an amplified library (Release Notes)|
|pbmm2||Y||Y||A minimap2 frontend for PacBio native data formats (Release Notes)|
|pbsv||Y||-||Structural variant analysis (Release Notes)|
|recalladapters||Y||-||Recall adapters (Release Notes)|
|zmwfilter||Y||-||Filter reads on ZMW ID(s)|
These combine multiple repos into a single bioconda package.
|pb-falcon||Y||-||pypeflow/FALCON/FALCON_unzip (Release Notes)|
|pb-dazzler||Y||Y||PacBio forks of DALIGNER/DAMASKER/DAZZ_DB/DEXTRACTOR|
These include dependencies only. They describe a mutually consistent, well-tested set of versions of all dependencies.
|pb-assembly||Y||-||Everything needed to run Falcon and Unzip (Release Notes)|
Where do I get support?
PacBio tools distributed via bioconda are not covered by any service level agreement or the like. As such, please do not contact a PacBio Field Applications Scientist or PacBio Customer Service for assistance with any bioconda releases. We instead provide an issue tracker for you to report issues.
I can't find tool X, when will it be available on bioconda?
We do not provide ETAs for currently not available tools.
When will a new version of tool X be available?
We do not provide ETAs for our release schedule.
Will SMRT Link be available on bioconda?
There are no plans. For the latest SMRT Link release, please refer to currently available SMRT Link downloads.
Can I get the exact version of the binaries from SMRT Link version XY through bioconda?
There is no effort to keep official SMRT Link releases and bioconda binaries in sync.
Which version of tool X shall I use, from bioconda or from SMRT Link?
If you need ISO-compliant software that has been fully vetted, you must use our official SMRT Link software. Bioconda binaries are pre-release versions that adhere to high standards, but might generate slightly different output, due to bug fixes and/or new features.
Why is the official SMRT Tools Guide not in sync with bioconda binaries?
Official documentation provided by PacBio is for binaries distributed in stable SMRT Link releases. You can click on package names in the table above to get to unofficial, best effort documentation. Combo- and meta-packages don't necessarily have additional documentation, as they serve as lightweight, yet well-tested, sets of existing packages.
Which operating systems are supported?
All packages are available for 64-bit linux. Some are available for 64-bit MacOS. For details, please study the table above. There are no plans to provide darwin binaries for packages currently missing MacOS. There are no plans to provide executables for Windows. We do not provide support for WSL (Windows Subsystem for Linux).
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