2019
DOI: 10.1371/journal.pcbi.1006790
|View full text |Cite
|
Sign up to set email alerts
|

Apollo: Democratizing genome annotation

Abstract: Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing a… Show more

Help me understand this report
View preprint versions

Search citation statements

Order By: Relevance

Paper Sections

Select...
1
1
1
1

Citation Types

0
184
0

Year Published

2019
2019
2024
2024

Publication Types

Select...
4
4
1

Relationship

0
9

Authors

Journals

citations
Cited by 209 publications
(193 citation statements)
references
References 46 publications
0
184
0
Order By: Relevance
“…The future development and continued support of this and other such initiatives should help the lab-based researchers complete a good first draft of a genome annotation efficiently without major resource implications. Furthermore, recent developments in the Apollo pipeline [130], integrated within databases such as VEuPathDB [131], allows researchers to inspect and modify genome features efficiently and can also be utilised in private workspaces. Data can remain private to a specific work group and be transferred to public databases when appropriate.…”
Section: Opportunities and Challenges In Getting Value From Fungal Ommentioning
confidence: 99%
“…The future development and continued support of this and other such initiatives should help the lab-based researchers complete a good first draft of a genome annotation efficiently without major resource implications. Furthermore, recent developments in the Apollo pipeline [130], integrated within databases such as VEuPathDB [131], allows researchers to inspect and modify genome features efficiently and can also be utilised in private workspaces. Data can remain private to a specific work group and be transferred to public databases when appropriate.…”
Section: Opportunities and Challenges In Getting Value From Fungal Ommentioning
confidence: 99%
“…Non-coding RNA were predicted with tRNAscan-SE [95], RNAmmer [96] and Infernal [97] using the Rfam database [98]. The obtained data were integrated in an instance of the genome viewer Apollo [99] allowing experts to validate gene prediction quality and perform manual curation.…”
Section: Genome Annotation Of the Four Newly Sequenced Genomesmentioning
confidence: 99%
“…The overall annotation strategy is presented in Additional file 1: Figure S6 and consisted of four key stages: (i) RNAseq evidence was used to train ab initio gene finding using Braker [35] ; (ii) full-length high-quality isoforms generated using Iso-Seq were used to identify candidate gene models using the annotation tool Program to Assemble Spliced Alignments (PASA; [36] ; (iii) evidence from steps (i) and (ii), together with 110 manually curated genes and orthologs from the C. elegans and H. contortus V1 genomes, were incorporated using EvidenceModeller; and finally (iv) UTRs and multi-evidence gene models were updated using the full-length isoforms once again using PASA. We further curated the genome annotation using Apollo [37] ; together, this strategy achieved a high level of sensitivity and precision based on comparison with a subset of manually curated genes ( Additional file 2: Table S5 ).…”
Section: Generation Of a High-quality Transcriptome Annotation Incorpmentioning
confidence: 99%
“…The genome annotation, as well as available evidence used to generate the annotation (including per life stage RNAseq, Iso-Seq [full-length high quality & CCS reads], coverage and repeat tracks), was uploaded to the web portal Apollo[37] for further visualisation and manual curation. This platform has been used to provide a means to continually improve the H. contortus genome annotation via manual curation as new information becomes available.…”
mentioning
confidence: 99%