virnet
DeePhage
| virnet | DeePhage | |
|---|---|---|
| 1 | 1 | |
| 29 | 19 | |
| - | - | |
| 0.0 | 3.9 | |
| over 2 years ago | 6 months ago | |
| Jupyter Notebook | MATLAB | |
| Apache License 2.0 | GNU Lesser General Public License v3.0 only |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
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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.
virnet
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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.
DeePhage
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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.
What are some alternatives?
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
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
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
Cenote_Unlimited_Breadsticks - DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
virMine