PPR-Meta
A tool for identifying phages and plasmids from metagenomic fragments using deep learning (by zhenchengfang)
virnet
VirNet: A deep attention model for viral reads identification (by alyosama)
| PPR-Meta | virnet | |
|---|---|---|
| 1 | 1 | |
| 34 | 29 | |
| - | - | |
| 1.8 | 0.0 | |
| about 3 years ago | over 2 years ago | |
| MATLAB | Jupyter Notebook | |
| GNU Lesser General Public License v3.0 only | Apache License 2.0 |
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.
PPR-Meta
Posts with mentions or reviews of PPR-Meta.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-18.
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Bad tools that NEED improvement
Deephage and PPR-meta: both by the same group. They require MATLAB which makes them tricky on an HPC or cloud system. They both say that if you need to run on several samples concurrently, you must clone the tool to a new directory for each(!). Likely due to temporary files being written to the working directory. Entirely unscalable in that case.
virnet
Posts with mentions or reviews of virnet.
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
VirNet: several issues with their dependencies not being available. For fun, you have to read the issue opened on their "requirments.txt". Pointed out bad dependencies, and mentioned that the file "requirments.txt" was mispelled and so didn't match the README. They updated the README to reflect the mispelling, left the bad file name and bad dependencies, and closed the issue.
What are some alternatives?
When comparing PPR-Meta and virnet you can also consider the following projects:
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers