PPR-Meta
RNN-VirSeeker
| PPR-Meta | RNN-VirSeeker | |
|---|---|---|
| 1 | 1 | |
| 34 | 8 | |
| - | - | |
| 1.8 | 0.0 | |
| about 3 years ago | over 2 years ago | |
| MATLAB | Python | |
| GNU Lesser General Public License v3.0 only | - |
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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
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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.
RNN-VirSeeker
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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.
What are some alternatives?
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
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.
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
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers