virnet
MetaRon
| virnet | MetaRon | |
|---|---|---|
| 1 | 1 | |
| 29 | 6 | |
| - | - | |
| 0.0 | 1.8 | |
| over 2 years ago | about 2 years ago | |
| Jupyter Notebook | Python | |
| Apache License 2.0 | GNU General Public License v3.0 or later |
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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.
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.
What are some alternatives?
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
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
Cenote_Unlimited_Breadsticks - DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
virMine
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.