virMine
RNN-VirSeeker
| virMine | RNN-VirSeeker | |
|---|---|---|
| 1 | 1 | |
| 18 | 8 | |
| - | - | |
| 0.0 | 0.0 | |
| about 2 years ago | over 2 years ago | |
| Python | Python | |
| MIT License | - |
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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VirMine: docker container can't be built due to outdated and unavailable dependencies.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.
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?
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
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
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