Cenote_Unlimited_Breadsticks
virMine
Cenote_Unlimited_Breadsticks | virMine | |
---|---|---|
1 | 1 | |
6 | 18 | |
- | - | |
2.7 | 0.0 | |
4 months ago | about 2 years ago | |
Shell | Python | |
MIT License | 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.
virMine
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Bad tools that NEED improvement
VirMine: docker container can't be built due to outdated and unavailable dependencies. Even with that resolved myself, they install a package that needs CLI input during container building which cannot be supplied so it gets stuck in a loop. Cannot be installed.
What are some alternatives?
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.
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
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