CAT statistics

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CAT specifications


Unique identifier OMICS_25173
Name CAT
Alternative name Comparative Annotation Toolkit
Interface Command line interface
Restrictions to use None
Input data A HAL alignment file, an existing annotation set, aligned RNA-seq reads.
Input format HAL
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Kent toolkit, bedtools, samtools, Augustus
Maintained Yes



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  • person_outline Benedict Paten <>

Publication for Comparative Annotation Toolkit

CAT in publication

PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] segments were merged into the final consensus. the nanopolish jobs were run using default parameters except the “–fix-homopolymers” and “–min-candidate-frequency 0.01” options were applied., comparative annotation toolkit (cat) ( was run on both the polished […]

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CAT institution(s)
Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA, USA; Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Pacific Biosciences of California, Inc., Menlo Park, CA, USA; European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
CAT funding source(s)
Supported by, in part, US National Institutes of Health (NIH) grants U24HG009081 and U41HG007635 and HG007990 and HG007234.

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