Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
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 assembl...
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| Published in | Genome research Vol. 28; no. 7; pp. 1029 - 1038 |
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| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Cold Spring Harbor Laboratory Press
01.07.2018
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1088-9051 1549-5469 1549-5469 |
| DOI | 10.1101/gr.233460.117 |
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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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| AbstractList | 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. 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.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. |
| Author | Fiddes, Ian T. Armstrong, Joel Haussler, David Diekhans, Mark Earl, Dent Paten, Benedict Gordon, David Eichler, Evan E. Stanke, Mario Kronenberg, Zev N. Underwood, Jason G. Keane, Thomas Nachtweide, Stefanie |
| AuthorAffiliation | 4 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA 5 Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA 2 10x Genomics, Pleasanton, California 94566, USA 6 Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA 1 Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA 3 Institute of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany 7 European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom |
| AuthorAffiliation_xml | – name: 3 Institute of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany – name: 4 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA – name: 7 European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom – name: 5 Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA – name: 1 Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA – name: 6 Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA – name: 2 10x Genomics, Pleasanton, California 94566, USA |
| Author_xml | – sequence: 1 givenname: Ian T. surname: Fiddes fullname: Fiddes, Ian T. – sequence: 2 givenname: Joel surname: Armstrong fullname: Armstrong, Joel – sequence: 3 givenname: Mark surname: Diekhans fullname: Diekhans, Mark – sequence: 4 givenname: Stefanie surname: Nachtweide fullname: Nachtweide, Stefanie – sequence: 5 givenname: Zev N. surname: Kronenberg fullname: Kronenberg, Zev N. – sequence: 6 givenname: Jason G. surname: Underwood fullname: Underwood, Jason G. – sequence: 7 givenname: David surname: Gordon fullname: Gordon, David – sequence: 8 givenname: Dent surname: Earl fullname: Earl, Dent – sequence: 9 givenname: Thomas surname: Keane fullname: Keane, Thomas – sequence: 10 givenname: Evan E. surname: Eichler fullname: Eichler, Evan E. – sequence: 11 givenname: David surname: Haussler fullname: Haussler, David – sequence: 12 givenname: Mario surname: Stanke fullname: Stanke, Mario – sequence: 13 givenname: Benedict surname: Paten fullname: Paten, Benedict |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29884752$$D View this record in MEDLINE/PubMed |
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| Copyright | 2018 Fiddes et al.; Published by Cold Spring Harbor Laboratory Press. Copyright Cold Spring Harbor Laboratory Press Jul 2018 2018 |
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| SubjectTerms | Algorithms Animals Annotations Genome, Human - genetics Genomes High-Throughput Nucleotide Sequencing - methods Humans Isoforms Method Molecular Sequence Annotation - methods Orthology Rats Ribonucleic acid RNA RNA - genetics |
| Title | Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation |
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