Cenote_Unlimited_Breadsticks
PhaMers
| Cenote_Unlimited_Breadsticks | PhaMers | |
|---|---|---|
| 1 | 1 | |
| 6 | 6 | |
| - | - | |
| 2.7 | 10.0 | |
| 4 months ago | almost 5 years ago | |
| Shell | Python | |
| MIT License | GNU General Public License v3.0 or later |
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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.
PhaMers
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Bad tools that NEED improvement
PhaMers: several open issues. I opened the one about bad FASTA header parsing. But even when I reformat my headers so that works, new errors pop up (which I didn't bother opening issues for since they were unresponsive to others). Also, output is written to current working directory which is annoying.
What are some alternatives?
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
virMine
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
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.
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.