Back

Covidex: an ultrafast and accurate tool for virus subtyping

Cacciabue, M.; Aguilera, P.; Gismondi, M. I.; Taboga, O.

2020-08-21 bioinformatics
10.1101/2020.08.21.261347 bioRxiv
Show abstract

Covidex is an open-source, alignment-free machine learning subtyping tool for viral species. It is a shiny app that allows a fast and accurate classification in pre-defined clusters for SARS-CoV-2 and FMDV genome sequences. The user can also build its own classification models with the Covidex model generator. AvailabilityCovidex is open-source, cross-platform compatible, and is available under the terms of the GNU General Public License v3 (http://www.gnu.org/licenses/gpl.txt). Covidex is available via SourceForge https://sourceforge.net/projects/covidex or the web application https://cacciabue.shinyapps.io/shiny2/ Contactcacciabue.marco@inta.gob.ar; marcocacciabue@yahoo.com

Matching journals

The top 2 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.3%
39.3%
Similar papers in this journal
2
Bioinformatics Advances
◐ 203 papers in training set
Top 0.2%
11.8%
Similar papers in this journal
50% of probability mass above
3
Virus Evolution
◐ 155 papers in training set
Top 0.2%
11.8%
Similar papers in this journal
4
BMC Bioinformatics
○ 457 papers in training set
Top 2%
5.1%
Similar papers in this journal
5
PeerJ
◐ 308 papers in training set
Top 2%
4.0%
Similar papers in this journal
6
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.4%
7
Viruses
○ 332 papers in training set
Top 3%
1.7%
8
Journal of Open Source Software
● 25 papers in training set
Top 0.2%
1.5%
9
Frontiers in Bioinformatics
○ 49 papers in training set
Top 0.7%
1.3%
10
Methods in Ecology and Evolution
○ 176 papers in training set
Top 1%
1.3%
11
Nucleic Acids Research
◐ 1281 papers in training set
Top 12%
1.0%
12
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
1.0%
13
Peer Community Journal
● 281 papers in training set
Top 5%
0.9%
14
F1000Research
○ 88 papers in training set
Top 4%
0.8%
15
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 7%
0.8%
16
Frontiers in Genetics
○ 230 papers in training set
Top 6%
0.6%
17
Molecular Biology and Evolution
◐ 542 papers in training set
Top 6%
0.6%
18
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.4%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.