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Consensus library and applications
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README.md

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Unanimity

C++ library and its applications to generate and process accurate consensus sequences


Availability

Latest ccs can be installed via bioconda package pbccs.

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

Circular Consensus Calling

ccs takes multiple reads of the same SMRTbell sequence and combines them, employing a statistical model, to produce one high quality consensus sequence. More information available here.

FAQ

Help! I am getting "Unsupported chemistries found: (...)"!

Similar to pbbam, Unanimity's consensus models require chemistry-dependent parameters. As part of ongoing development efforts, we might need to introduce new part numbers to identify novel reagents and/or SMRT Cells. If your version of Unanimity significantly predates the chemistry you have used for generating collections of data, you will run into issues with Unanimity not being able to handle your data. In such cases, download the latest version of the model parameters and place them in a subdirectory of ${SMRT_CHEMISTRY_BUNDLE_DIR}:

cd <some persistent dir, preferably the same as used for pbbam>
export SMRT_CHEMISTRY_BUNDLE_DIR="${PWD}"

mkdir -p arrow
cp /some/download/dir/model.json arrow/

This will cause Unanimity to try to load models from all files in ${SMRT_CHEMISTRY_BUNDLE_DIR}/arrow with a .json suffix.

Changelog

  • 3.4.1:
    • Log used chemistry model to INFO level
  • 3.4.0:
    • Fixes to unpolished mode for IsoSeq
    • Improve runtime when --minPredictedAccuracy has been increased
  • 3.3.0:
    • Add a windowing approach to reduce computational complexity from quadratic to linear
    • Improve multi-threading framework to increase throughput
    • Enhance XML output, propagate CollectionMetadata
    • Includes latest chemistry parameters
  • 3.1.0:
    • Add --maxPoaCoverage to decrease runtime for unpolished output, special parameter for IsoSeq workflow
    • Chemistry parameters for SMRT Link v6.0

License

PacBio open source 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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