PhaMers
virMine
PhaMers | virMine | |
---|---|---|
1 | 1 | |
6 | 18 | |
- | - | |
10.0 | 0.0 | |
almost 5 years ago | about 2 years ago | |
Python | Python | |
GNU General Public License v3.0 or later | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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.
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VirMine: docker container can't be built due to outdated and unavailable dependencies.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.
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
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
virnet - VirNet: A deep attention model for viral reads identification
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
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
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning