PPR-Meta
A tool for identifying phages and plasmids from metagenomic fragments using deep learning (by zhenchengfang)
PhaMers
A bioinformatic tool for identifying bacteriophages using machine learning and k-mers (by jondeaton)
| PPR-Meta | PhaMers | |
|---|---|---|
| 1 | 1 | |
| 34 | 6 | |
| - | - | |
| 1.8 | 10.0 | |
| about 3 years ago | almost 5 years ago | |
| MATLAB | Python | |
| GNU Lesser General Public License v3.0 only | 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.
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.
-
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.
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 PPR-Meta and PhaMers 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.
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
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
virnet - VirNet: A deep attention model for viral reads identification