MetaRon
RNN-VirSeeker
MetaRon | RNN-VirSeeker | |
---|---|---|
1 | 1 | |
6 | 8 | |
- | - | |
1.8 | 0.0 | |
about 2 years ago | over 2 years ago | |
Python | Python | |
GNU General Public License v3.0 or later | - |
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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.
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?
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
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
virMine
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
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
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.