Augustus
Genome annotation with AUGUSTUS (by Gaius-Augustus)
Liftoff
An accurate GFF3/GTF lift over pipeline (by agshumate)
| Augustus | Liftoff | |
|---|---|---|
| 1 | 2 | |
| 264 | 391 | |
| 2.7% | - | |
| 5.0 | 5.2 | |
| 13 days ago | 10 months ago | |
| C++ | Python | |
| - | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Augustus
Posts with mentions or reviews of Augustus.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-02-15.
-
Cross-species functional annotation?
I use the Augustus tool to annotate a genome. You can give it a species to base the annotation model on. https://github.com/Gaius-Augustus/Augustus
Liftoff
Posts with mentions or reviews of Liftoff.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-02-06.
-
Identifying potential genes involved in nociception
How distant is your study organism to Drosophila? You mention it's another model organism but I can't think of any others that are close to flies. If you have a close-ish organism you could try a 'lift' of the annotations from Drosophila to your draft genome (I like 'liftoff' for this). This tries to match across genes from your input reference (Drosophila) to your draft genome. This works best when the 2 organisms are somewhat closely related. You can then look up where those 'painless' genes in your draft organism's reference, and this info can also be used to inform your transcriptome analysis.
- Cross-species functional annotation?
What are some alternatives?
When comparing Augustus and Liftoff you can also consider the following projects:
deeplabel - A cross-platform desktop image annotation tool for machine learning
miniprot - Align proteins to genomes with splicing and frameshift
ksnip - ksnip the cross-platform screenshot and annotation tool
htm.core - Actively developed Hierarchical Temporal Memory (HTM) community fork (continuation) of NuPIC. Implementation for C++ and Python
ksnip - ksnip the cross-platform screenshot and annotation tool [Moved to: https://github.com/ksnip/ksnip]
PGA - Plastid Genome Annotator
frugally-deep - A lightweight header-only library for using Keras (TensorFlow) models in C++.