PacBio Secondary Analysis Tools on Bioconda
Information
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.
Support
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.
File sharing
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 [email protected] and proceed to upload your files. More info about file transfer security.
Installation
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_namePackages can be updated with:
> conda update package_nameIn 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 --allIn order to avoid stale dependencies in the dependency graph.
Availability
Notes:
- 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
Packages
| Package | Linux | Mac | Description |
|---|---|---|---|
| isoseq | Y | - | Scalable de novo isoform discovery (Release Notes) |
| jasmine | Y | - | Predict 5mC in PacBio HiFi reads (Release Notes) |
| lima | Y | - | Demultiplex barcoded samples (Release Notes) |
| pbaa | Y | Y | HiFi specific Amplicon Analysis |
| pbbam | Y | Y | BAM C++ library, tools are now in pbtk (Release Notes) |
| pbccs | Y | - | Generate HiFi reads for Sequel II (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 dataset) |
| pbfusion | Y | - | A fusion gene detection tool for all Iso-Seq data types (Release Notes) |
| pbipa | Y | - | Construct very contiguous, high quality de novo genome assemblies using the IPA HiFi assembler. (Release Notes) |
| pbmarkdup | Y | - | Mark duplicate reads from PacBio sequencing of an amplified library (Release Notes) |
| pbmm2 | Y | - | A minimap2 frontend for PacBio native data formats (Release Notes) |
| pbpigeon | Y | - | PacBio transcript toolkit (Release Notes) |
| pbskera | Y | - | Read deconcatination (Release Notes) |
| pbsv | Y | - | Structural variant analysis (Release Notes) |
| pbtk | Y | - | PacBio BAM toolkit contains bam2fasta, bam2fastq, ccs-kinetics-bystrandify, extracthifi, pbindex, pbindexdump, pbmerge, zmwfilter (Release Notes) |
| recalladapters | Y | - | Recall adapters (Release Notes) |
| trgt | Y | - | Tandem repeat genotyping and visualization (Release Notes) |
Combo-Packages
These combine multiple repos into a single bioconda package.
| Package | Linux | Mac | Description |
|---|---|---|---|
| pb-falcon | Y | - | pypeflow/FALCON/FALCON_unzip (Release Notes) |
Available Meta-Packages
These include dependencies only. They describe a mutually consistent, well-tested set of versions of all dependencies.
| Package | Linux | Mac | Description |
|---|---|---|---|
| pb-assembly | Y | - | Everything needed to run Falcon and Unzip (Release Notes) |
FAQ
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).
Disclaimer/Copyright
© Copyright Pacific Biosciences of California, Inc. All rights reserved. Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, SMRTbell, Iso-Seq and Sequel are trademarks of Pacific Biosciences. All other trademarks are the sole property of their respective owners. Certain notices, terms, conditions and/or use restrictions may pertain to your use of Pacific Biosciences products and/or third party products. Please refer to the applicable Pacific Biosciences Terms and Conditions of Sale and to the applicable license terms at http://www.pacb.com/legal-and-trademarks/product-license-and-use-restrictions/. Information herein is subject to change without notice. Pacific Biosciences assumes no responsibility for any errors or omissions herein.
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