Apollo 3: Multi-Species Genome Curation

Abstract

We present Apollo 3, a new manual genome annotation tool that integrates with the JBrowse 2 genome browser. Its functionality is inspired by existing manual genome annotation tools such as Apollo, Artemis, and Otter, but uses an updated and more scalable architecture and technology stack. It allows the simultaneous editing of multiple genomes, including the visualization of synteny to inform those annotations. Apollo 3 can be used as a standalone annotation editor, or it can be installed on a server and used collaboratively. We describe the application's design, features, and use cases.

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BibTeX RIS

BibTeX

@misc{stevens2026apollo,
  title = {{Apollo 3: Multi-Species Genome Curation}},
  author = {G. J. Stevens and K. Sutinen and D. Beraldi and S. Budhanuru Ramaraju and C. M. Diesh and W. Haese-Hill and P. Xie and C. Bridge and A. Morison and A. Leung and U. Böhme and S. Cain and N. Dunn and T. Hunt and J. E. Loveland and A. Frankish and A. Papanicolau and S. Giorgetti and J. Keatley and B. Flint and L. D. Stein and R. Buels and M. Berriman and I. Holmes},
  howpublished = {bioRxiv},
  year = {2026},
  month = jun,
  doi = {10.64898/2026.06.08.730970},
  url = {https://www.biorxiv.org/content/10.64898/2026.06.08.730970v2},
  note = {CC BY},
}

RIS

TY  - UNPB
TI  - Apollo 3: Multi-Species Genome Curation
AU  - G. J. Stevens
AU  - K. Sutinen
AU  - D. Beraldi
AU  - S. Budhanuru Ramaraju
AU  - C. M. Diesh
AU  - W. Haese-Hill
AU  - P. Xie
AU  - C. Bridge
AU  - A. Morison
AU  - A. Leung
AU  - U. Böhme
AU  - S. Cain
AU  - N. Dunn
AU  - T. Hunt
AU  - J. E. Loveland
AU  - A. Frankish
AU  - A. Papanicolau
AU  - S. Giorgetti
AU  - J. Keatley
AU  - B. Flint
AU  - L. D. Stein
AU  - R. Buels
AU  - M. Berriman
AU  - I. Holmes
PY  - 2026
DA  - 2026/06/08
PB  - bioRxiv
DO  - 10.64898/2026.06.08.730970
UR  - https://www.biorxiv.org/content/10.64898/2026.06.08.730970v2
AB  - We present Apollo 3, a new manual genome annotation tool that integrates with the JBrowse 2 genome browser. Its functionality is inspired by existing manual genome annotation tools such as Apollo, Artemis, and Otter, but uses an updated and more scalable architecture and technology stack. It allows the simultaneous editing of multiple genomes, including the visualization of synteny to inform those annotations. Apollo 3 can be used as a standalone annotation editor, or it can be installed on a server and used collaboratively. We describe the application's design, features, and use cases.
ER  -

Abstract

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