ViraMiner
CNN based classifier for detecting viral sequences among metagenomic contigs (by NeuroCSUT)
Cenote_Unlimited_Breadsticks
DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report (by mtisza1)
| ViraMiner | Cenote_Unlimited_Breadsticks | |
|---|---|---|
| 1 | 1 | |
| 28 | 6 | |
| - | - | |
| 10.0 | 2.7 | |
| over 3 years ago | 4 months ago | |
| Python | Shell | |
| - | MIT License |
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.
ViraMiner
Posts with mentions or reviews of ViraMiner.
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
ViraMiner: bad documentation. Wasnt sure how to install or run it. Maybe it works? Never got that far.
Cenote_Unlimited_Breadsticks
Posts with mentions or reviews of Cenote_Unlimited_Breadsticks.
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
Cenote Unlimited Breadsticks: I have run ~160k simulated contigs of various lengths through this tool, and none have been predicted as phage. I haven't openened an issue yet because I need to make sure it isn't on my end and that I can give a reprex. Also, you cannot choose the output directory, so it clutters your working directory.
What are some alternatives?
When comparing ViraMiner and Cenote_Unlimited_Breadsticks you can also consider the following projects:
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
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.