VirusSeeker-Virome
VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin. (by guoyanzhao)
DeePhage
A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning (by shufangwu)
| VirusSeeker-Virome | DeePhage | |
|---|---|---|
| 1 | 1 | |
| 16 | 19 | |
| - | - | |
| 10.0 | 3.9 | |
| over 6 years ago | 6 months ago | |
| Perl | MATLAB | |
| GNU General Public License v3.0 only | GNU Lesser General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
VirusSeeker-Virome
Posts with mentions or reviews of VirusSeeker-Virome.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-18.
-
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.
DeePhage
Posts with mentions or reviews of DeePhage.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-18.
-
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?
When comparing VirusSeeker-Virome and DeePhage you can also consider the following projects:
virMine
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
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers