VirusSeeker-Virome vs MetaRon

VirusSeeker-Virome

VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin. (by guoyanzhao)

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MetaRon

Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data. (by zaidissa)

metagenomics metagenomic-operons metagenomic-pipeline metagenomic-data-processing

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VirusSeeker-Virome		MetaRon
	Project
1	Mentions	1
16	Stars	6
-	Growth	-
10.0	Activity	1.8
over 6 years ago	Latest Commit	about 2 years ago
Perl	Language	Python
GNU General Public License v3.0 only	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.

VirusSeeker-Virome

Posts with mentions or reviews of VirusSeeker-Virome. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.

Bad tools that NEED improvement
11 projects | /r/bioinformatics | 18 Dec 2021

VirusSeeker: no installation or running instructions on GitHub. They do have it on their lab website, but you have to edit source files to point to databases. Too much of a pain. So not sure how it works once that is done.

MetaRon

Posts with mentions or reviews of MetaRon. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.

Bad tools that NEED improvement
11 projects | /r/bioinformatics | 18 Dec 2021

MetaRon is a tool for metagenomic operon prediction that was published in BMC Genomics in 2020. As far as I can tell, no one has been able to get it to work, and the authors are unresponsive on GitHub. If I knew any python, I would take a crack at fixing it.

What are some alternatives?

When comparing VirusSeeker-Virome and MetaRon you can also consider the following projects:

virMine

RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.

DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning

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

virnet - VirNet: A deep attention model for viral reads identification

PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers

ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs

PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning