DeePhage
Cenote_Unlimited_Breadsticks
| DeePhage | Cenote_Unlimited_Breadsticks | |
|---|---|---|
| 1 | 1 | |
| 19 | 6 | |
| - | - | |
| 3.9 | 2.7 | |
| 6 months ago | 4 months ago | |
| MATLAB | Shell | |
| GNU Lesser General Public License v3.0 only | MIT License |
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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.
Cenote_Unlimited_Breadsticks
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Bad tools that NEED improvement
Cenote Unlimited Breadsticks: I have run ~160k simulated contigs of various lengths through this tool, and none have been predicted as phage. I haven't openened an issue yet because I need to make sure it isn't on my end and that I can give a reprex. Also, you cannot choose the output directory, so it clutters your working directory.
What are some alternatives?
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
virnet - VirNet: A deep attention model for viral reads identification
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
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
virMine
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs