Prokka Alternatives

Similar projects and alternatives to prokka

Prodigal

4 400 0.0 C prokka VS Prodigal

Prodigal Gene Prediction Software
reCOGnizer

9 24 7.4 HTML prokka VS reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database
WorkOS

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The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
spades

4 659 2.7 C++ prokka VS spades

SPAdes Genome Assembler
mantis

6 51 3.1 Python prokka VS mantis

A package to annotate protein sequences (by PedroMTQ)
dfast_core

2 71 5.0 Python prokka VS dfast_core

DDBJ Fast Annotation and Submission Tool
bakta

1 386 8.5 Python prokka VS bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
BRAKER

2 318 8.8 Perl prokka VS 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
InfluxDB

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Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
funannotate

2 288 7.0 Python prokka VS funannotate

Eukaryotic Genome Annotation Pipeline

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better prokka alternative or higher similarity.

Suggest an alternative to prokka

prokka reviews and mentions

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.

orfs in DNA
3 projects | /r/bioinformatics | 11 Oct 2022

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).
Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
5 projects | /r/bioinformatics | 15 Nov 2021

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
ORF prediction for non-model organism with DNA sequence only
4 projects | /r/bioinformatics | 26 Sep 2021

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.
Genome analysis cost
2 projects | /r/bioinformatics | 3 Sep 2021

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.
A note from our sponsor - WorkOS
workos.com | 19 Apr 2024

The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning. Learn more →