bakta
prokka
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| bakta | prokka | |
|---|---|---|
| 1 | 5 | |
| 389 | 754 | |
| - | - | |
| 8.5 | 0.0 | |
| about 2 months ago | 19 days ago | |
| Python | Perl | |
| GNU General Public License v3.0 only | - |
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bakta
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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).
prokka
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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.
What are some alternatives?
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
Prodigal - Prodigal Gene Prediction Software
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
spades - SPAdes Genome Assembler
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
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
QUEEN - QUEEN: a framework to generate quinable and efficiently editable nucleotide sequence resources
funannotate - Eukaryotic Genome Annotation Pipeline
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
mantis - A package to annotate protein sequences