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




No version available



  • person_outline Benedict Paten

Publication for Comparative Annotation Toolkit

CAT citation


Nanopore sequencing and assembly of a human genome with ultra long reads

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

[…] Comparative Annotation Toolkit (CAT) ( was run on both the polished and unp […]

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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