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Cited by 120Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsBioinformatics and Genomic Networks

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

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Fiddes, Ian T., Armstrong, Joel, Diekhans, Mark, Nachtweide, Stefanie, Kronenberg, Zev N., Underwood, Jason G., Gordon, David, Earl, Dent +5 more·2018·Genome Research
DOI 10.1101/gr.233460.117PMC PMC6028123

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Abstract

The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation. We describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. We demonstrate the resulting discovery of novel genes, isoforms, and structural variants—even in genomes as well studied as rat and the great apes—and how these annotations improve cross-species RNA expression experiments.

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    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [9]

  • Alignments of such assemblies are essential for annotation and variant characterization.

    “Alignments of such assemblies are essential for annotation9 and variant characterization42 and should prove useful for reference-free pangenome construction of the variation present in a population43.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [9]

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Cited by

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Authors
Fiddes, I. T., Armstrong, J., Diekhans, M., Nachtweide, S., Kronenberg, Z. N., Underwood, J. G., Gordon, D., Earl, D., Keane, T., Eichler, E. E., Haussler, D., Stanke, M., & Paten, B.
Affiliations
  • Howard Hughes Medical Institute (US)
  • Universität Greifswald (DE)
  • University of Washington (US)
  • European Bioinformatics Institute (GB)
Corresponding author
Paten, Benedict
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2018-06-08
Volume
28
Issue
7
Pages
1029-1038
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.233460.117
PMC
PMC6028123
OpenAlex
W2952306768
Cited by
120
References
2
Citations by year
2026: 16 · 2025: 19 · 2024: 24 · 2023: 13 · 2022: 13 · 2021: 9 · 2020: 11 · 2019: 7 · 2018: 7
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • US National Institutes of Health (U24HG009081, U41HG007635, HG007990, HG007234)
  • Howard Hughes Medical Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
genome annotation, orthology, de novo genome assembly, rat genome, great apes, mammalian genomes, personal genome, novel genes, protein isoforms, structural variants
MeSH terms
Algorithms, Animals, Humans, RNA, Genome, Human, Rats, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing

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