prokka
:zap: :aquarius: Rapid prokaryotic genome annotation (by tseemann)
mantis
A package to annotate protein sequences (by PedroMTQ)
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.
mantis
Posts with mentions or reviews of mantis.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-11-15.
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database for protein biological function association
You could use https://github.com/PedroMTQ/mantis
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How to get consensus annotations for a de novo orthogroup/ortholog analysis?
https://github.com/PedroMTQ/mantis Mantis works on protein level but it does address the consensus matter you mentioned
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
Hello, I'm the developer of Mantis (https://github.com/PedroMTQ/mantis). Mantis doesn't use a database for COGs specifically but it does output some of the IDs you mentioned (e.g., KOs, COGs). If this is important for your work I could consider creating a COG centric database (or at least format it to be natively compatible with Mantis). Anyhow, please check the GitHub page and message me or post an issue and I'll try to help out.
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Functional annotation of prokaryotic genomes
Thanks a lot! Will definitely try it out. Another question: Does Mantis+eggNOG annotate the genes with eggNOG-ortholog-ids? More generally, what are the resulting annotation types? (pfam, GO, KO, EC and description are listed, how about KR, BiGG, brite and cazy?)
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How can I map KEGG gene categories onto aligned genomes?
You could accomplish this by gene calling with prodigal and then annotating with a tools like Mantis https://github.com/PedroMTQ/mantis
What are some alternatives?
When comparing prokka and mantis you can also consider the following projects:
Prodigal - Prodigal Gene Prediction Software
Biopython - Official git repository for Biopython (originally converted from CVS)
spades - SPAdes Genome Assembler
Hail - Cloud-native genomic dataframes and batch computing
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
dfast_core - DDBJ Fast Annotation and Submission Tool
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
funannotate - Eukaryotic Genome Annotation Pipeline
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database