BRAKER
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes (by Gaius-Augustus)
funannotate
Eukaryotic Genome Annotation Pipeline (by nextgenusfs)
| BRAKER | funannotate | |
|---|---|---|
| 2 | 2 | |
| 321 | 289 | |
| 1.9% | - | |
| 8.7 | 6.6 | |
| 9 days ago | 28 days ago | |
| Perl | Python | |
| GNU General Public License v3.0 or later | BSD 2-clause "Simplified" License |
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.
BRAKER
Posts with mentions or reviews of BRAKER.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-05.
-
Annotation of fungal genomes
Braker looks reasonable, though I only really have been doing bacterial genome annotation.
-
ORF prediction for non-model organism with DNA sequence only
BRAEKR2 (include GeneMark + AUGUSTUS, can take RNA-seq and OrthoDB in consideration)
funannotate
Posts with mentions or reviews of funannotate.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-05.
-
Annotation of fungal genomes
funannotate is an annotation package designed for fungi, but also works for eukaryotes too.
-
If you’re going to publish a tool, please actively maintain it, put up a hiatus notice, or discontinue it. . .
While we are at it, Jon Palmer, the maintainer/author of Funannotate, is very responsive, super nice, and maintains an extremely complicated code base.
What are some alternatives?
When comparing BRAKER and funannotate you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
Prodigal - Prodigal Gene Prediction Software
TRUST4 - TCR and BCR assembly from RNA-seq data
bracer - BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data