virMine
PPR-Meta
virMine | PPR-Meta | |
---|---|---|
1 | 1 | |
18 | 34 | |
- | - | |
0.0 | 1.8 | |
about 2 years ago | about 3 years ago | |
Python | MATLAB | |
MIT License | GNU Lesser General Public License v3.0 only |
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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VirMine: docker container can't be built due to outdated and unavailable dependencies.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.
PPR-Meta
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Bad tools that NEED improvement
Deephage and PPR-meta: both by the same group. They require MATLAB which makes them tricky on an HPC or cloud system. They both say that if you need to run on several samples concurrently, you must clone the tool to a new directory for each(!). Likely due to temporary files being written to the working directory. Entirely unscalable in that case.
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.
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
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
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