Cenote_Unlimited_Breadsticks
RNN-VirSeeker
| Cenote_Unlimited_Breadsticks | RNN-VirSeeker | |
|---|---|---|
| 1 | 1 | |
| 6 | 8 | |
| - | - | |
| 2.7 | 0.0 | |
| 4 months ago | over 2 years ago | |
| Shell | Python | |
| MIT License | - |
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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.
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?
virnet - VirNet: A deep attention model for viral reads identification
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
virMine
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
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