prokka
:zap: :aquarius: Rapid prokaryotic genome annotation (by tseemann)
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)
prokka | BRAKER | |
---|---|---|
5 | 2 | |
754 | 321 | |
- | 1.3% | |
0.0 | 8.7 | |
23 days ago | 6 days ago | |
Perl | Perl | |
- | 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.
prokka
Posts with mentions or reviews of prokka.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-11.
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orfs in DNA
If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
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ORF prediction for non-model organism with DNA sequence only
I just checked out Prokka, which uses Prodigal to predict genes. They do not seem to have any reservations for viruses. Thus, I recommend using Prokka directly, since that will conveniently add functional annotations.
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Genome analysis cost
If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.
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.
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Annotation of fungal genomes
Braker looks reasonable, though I only really have been doing bacterial genome annotation.
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ORF prediction for non-model organism with DNA sequence only
BRAEKR2 (include GeneMark + AUGUSTUS, can take RNA-seq and OrthoDB in consideration)
What are some alternatives?
When comparing prokka and BRAKER you can also consider the following projects:
Prodigal - Prodigal Gene Prediction Software
spades - SPAdes Genome Assembler
funannotate - Eukaryotic Genome Annotation Pipeline
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
dfast_core - DDBJ Fast Annotation and Submission Tool
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
mantis - A package to annotate protein sequences