ArticleGenome research2018
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
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- A complete genome for the common marmoset.Cell · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.Cell genomics · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.Scientific reports · 2026Article
- Prenatal maternal immune activation triggers lasting cell-specific transcriptomic dysregulation in the amygdala of primate offspring.Molecular psychiatry · 2026Article
- CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates.Genome biology · 2026Article
- The diploid reference genome of a human embryonic stem cell line.bioRxiv : the preprint server for biology · 2026Article
- A Complete Genome for the Common Marmoset.bioRxiv : the preprint server for biology · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
- Article
- Boundary-associated propagation of a processed pseudogene dissects pre-existing limitations of genome annotation in the T2T era.Mobile DNA · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- Pangenome graph analysis reveals evolution of resistance breaking in spinach downy mildew.PLoS biology · 2026Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.