PhaMers
RNN-VirSeeker
PhaMers | RNN-VirSeeker | |
---|---|---|
1 | 1 | |
6 | 8 | |
- | - | |
10.0 | 0.0 | |
almost 5 years ago | over 2 years ago | |
Python | Python | |
GNU General Public License v3.0 or later | - |
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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.
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?
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
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
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