RNN-VirSeeker
This is a deep learning method for identification of viral contigs with short length from metagenomic data. (by crazyinter)
PhaMers
A bioinformatic tool for identifying bacteriophages using machine learning and k-mers (by jondeaton)
| RNN-VirSeeker | PhaMers | |
|---|---|---|
| 1 | 1 | |
| 8 | 6 | |
| - | - | |
| 0.0 | 10.0 | |
| over 2 years ago | almost 5 years ago | |
| Python | Python | |
| - | 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.
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.
RNN-VirSeeker
Posts with mentions or reviews of RNN-VirSeeker.
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
RNN-Virseeker: hard coded paths to training and actual data, so source code must be edited for it to be used. Bad practice and unscalable. Also, they don't follow Python conventions. test.py is generally meant to indicate a unit/integration test file for something like pytest, but in their "tool" that is the actual tool's file name.
PhaMers
Posts with mentions or reviews of PhaMers.
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
PhaMers: several open issues. I opened the one about bad FASTA header parsing. But even when I reformat my headers so that works, new errors pop up (which I didn't bother opening issues for since they were unresponsive to others). Also, output is written to current working directory which is annoying.
What are some alternatives?
When comparing RNN-VirSeeker and PhaMers you can also consider the following projects:
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments 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
virMine
virnet - VirNet: A deep attention model for viral reads identification
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning