virnet
PhaMers
virnet | PhaMers | |
---|---|---|
1 | 1 | |
29 | 6 | |
- | - | |
0.0 | 10.0 | |
over 2 years ago | almost 5 years ago | |
Jupyter Notebook | Python | |
Apache License 2.0 | GNU General Public License v3.0 or later |
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.
virnet
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Bad tools that NEED improvement
VirNet: several issues with their dependencies not being available. For fun, you have to read the issue opened on their "requirments.txt". Pointed out bad dependencies, and mentioned that the file "requirments.txt" was mispelled and so didn't match the README. They updated the README to reflect the mispelling, left the bad file name and bad dependencies, and closed the issue.
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.
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
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.
Cenote_Unlimited_Breadsticks - DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
virMine
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.