MetaRon
Cenote_Unlimited_Breadsticks
| MetaRon | Cenote_Unlimited_Breadsticks | |
|---|---|---|
| 1 | 1 | |
| 6 | 6 | |
| - | - | |
| 1.8 | 2.7 | |
| about 2 years ago | 4 months ago | |
| Python | Shell | |
| GNU General Public License v3.0 or later | MIT License |
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MetaRon
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Bad tools that NEED improvement
MetaRon is a tool for metagenomic operon prediction that was published in BMC Genomics in 2020. As far as I can tell, no one has been able to get it to work, and the authors are unresponsive on GitHub. If I knew any python, I would take a crack at fixing it.
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?
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
virnet - VirNet: A deep attention model for viral reads identification
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
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.