funannotate
Eukaryotic Genome Annotation Pipeline (by nextgenusfs)
bracer
BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data (by Teichlab)
| funannotate | bracer | |
|---|---|---|
| 2 | 2 | |
| 293 | 37 | |
| - | - | |
| 6.6 | 7.3 | |
| 12 days ago | about 1 month ago | |
| Python | Python | |
| BSD 2-clause "Simplified" License | GNU General Public License v3.0 or later |
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.
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.
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Annotation of fungal genomes
funannotate is an annotation package designed for fungi, but also works for eukaryotes too.
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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.
bracer
Posts with mentions or reviews of bracer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-03-11.
-
If you’re going to publish a tool, please actively maintain it, put up a hiatus notice, or discontinue it. . .
A perfect example of Nature Methods bit is bracer. I was so stoked they released it because it basically solved all the problems I was trying to do with an analysis. Couldn't get it installed for the life of me and no response from GitHub issues. Tried conda. Tried installing everything manually. Good thing TRUST4 was around to save the day and the maintainer was really responsive whenever I had questions.
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Any packages recommended for reconstruction of B cell receptor sequences from single-cell RNA-seq data?
I've been trying to install BraCeR but I can't get the dependencies to work together. Any other tools recommended?
What are some alternatives?
When comparing funannotate and bracer you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
BASIC - BASIC: BCR and TCR assembly from single cell RNA-seq
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
TRUST4 - TCR and BCR assembly from RNA-seq data