PhaMers
PPR-Meta
| PhaMers | PPR-Meta | |
|---|---|---|
| 1 | 1 | |
| 6 | 34 | |
| - | - | |
| 10.0 | 1.8 | |
| almost 5 years ago | about 3 years ago | |
| Python | MATLAB | |
| GNU General Public License v3.0 or later | GNU Lesser General Public License v3.0 only |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
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.
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?
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
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
virnet - VirNet: A deep attention model for viral reads identification
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.
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs