PPR-Meta
VirusSeeker-Virome
| PPR-Meta | VirusSeeker-Virome | |
|---|---|---|
| 1 | 1 | |
| 34 | 16 | |
| - | - | |
| 1.8 | 10.0 | |
| about 3 years ago | over 6 years ago | |
| MATLAB | Perl | |
| GNU Lesser General Public License v3.0 only | GNU General Public License v3.0 only |
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.
PPR-Meta
-
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.
VirusSeeker-Virome
-
Bad tools that NEED improvement
VirusSeeker: no installation or running instructions on GitHub. They do have it on their lab website, but you have to edit source files to point to databases. Too much of a pain. So not sure how it works once that is done.
What are some alternatives?
RNN-VirSeeker - This is a deep learning method for identification of viral contigs with short length from metagenomic data.
virMine
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
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
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.