virnet
Cenote_Unlimited_Breadsticks
| virnet | Cenote_Unlimited_Breadsticks | |
|---|---|---|
| 1 | 1 | |
| 29 | 6 | |
| - | - | |
| 0.0 | 2.7 | |
| over 2 years ago | 4 months ago | |
| Jupyter Notebook | Shell | |
| Apache License 2.0 | MIT License |
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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.
Cenote_Unlimited_Breadsticks
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Bad tools that NEED improvement
Cenote Unlimited Breadsticks: I have run ~160k simulated contigs of various lengths through this tool, and none have been predicted as phage. I haven't openened an issue yet because I need to make sure it isn't on my end and that I can give a reprex. Also, you cannot choose the output directory, so it clutters your working directory.
What are some alternatives?
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
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
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
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.
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
tolkien-char-prescription-drug - Bilbo, Silenor, Avandaryl, Nardil, Cymbalta. Only one of those is actually a Tolkien character. Could we solve this problem using artificial neural networks?
AllenSDK - code for reading and processing Allen Institute for Brain Science data