Cenote_Unlimited_Breadsticks
VirusSeeker-Virome
Cenote_Unlimited_Breadsticks | VirusSeeker-Virome | |
---|---|---|
1 | 1 | |
6 | 16 | |
- | - | |
2.7 | 10.0 | |
5 months ago | over 6 years ago | |
Shell | Perl | |
MIT License | GNU General Public License v3.0 only |
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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.
VirusSeeker-Virome
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Bad tools that NEED improvement
VirusSeeker: no installation or running instructions on GitHub. They do have it on their lab website, but you have to edit source files to point to databases. Too much of a pain. So not sure how it works once that is done.
What are some alternatives?
virnet - VirNet: A deep attention model for viral reads identification
virMine
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
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
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
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.