tetano
Editor, Senior Moderator
Bioinformatics. 2020 Feb 28. pii: btaa145. doi: 10.1093/bioinformatics/btaa145. [Epub ahead of print] [h=1]Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.[/h]
Cleemput S[SUP]1[/SUP], Dumon W[SUP]1[/SUP], Fonseca V[SUP]2,[/SUP][SUP]3,[/SUP][SUP]4[/SUP], Karim WA[SUP]2[/SUP], Giovanetti M[SUP]5[/SUP], Alcantara LC[SUP]3,[/SUP][SUP]5[/SUP], Deforche K[SUP]1[/SUP], de Oliveira T[SUP]2,[/SUP][SUP]6,[/SUP][SUP]7[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] [h=4]SUMMARY:[/h] Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.
[h=4]AVAILABILITY:[/h] https://www.genomedetective.com/app/typingtool/cov.
[h=4]SUPPLEMENTARY INFORMATION:[/h] Supplementary data are available at Bioinformatics online.
? The Author(s) 2020. Published by Oxford University Press.
PMID: 32108862 DOI: 10.1093/bioinformatics/btaa145
Cleemput S[SUP]1[/SUP], Dumon W[SUP]1[/SUP], Fonseca V[SUP]2,[/SUP][SUP]3,[/SUP][SUP]4[/SUP], Karim WA[SUP]2[/SUP], Giovanetti M[SUP]5[/SUP], Alcantara LC[SUP]3,[/SUP][SUP]5[/SUP], Deforche K[SUP]1[/SUP], de Oliveira T[SUP]2,[/SUP][SUP]6,[/SUP][SUP]7[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] [h=4]SUMMARY:[/h] Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.
[h=4]AVAILABILITY:[/h] https://www.genomedetective.com/app/typingtool/cov.
[h=4]SUPPLEMENTARY INFORMATION:[/h] Supplementary data are available at Bioinformatics online.
? The Author(s) 2020. Published by Oxford University Press.
PMID: 32108862 DOI: 10.1093/bioinformatics/btaa145