Difference between revisions of "VirusDetect"

Latest revision as of 23:22, 30 July 2020

Description

VirusDetect is a software package that can efficiently and exhaustively analyze large-scale sRNA datasets for virus identification. The program performs reference-guided assembly by aligning sRNA reads to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs are compared to the reference virus sequences for virus identification. The contigs were treated as undetermined contigs if they are not hit to any known viruses. The siRNA profile of these undetermined contigs are provided as guidance to discovery novel viruses which do not show sequence similarity with known viruses.

Environment Modules

Run module spider virusdetect to find out what environment modules are available for this application.

System Variables

HPC_VIRUSDETECT_DIR - installation directory
HPC_VIRUSDETECT_BIN - executable directory

Citation

If you publish research that uses virusdetect you have to cite it as follows:

Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling K-S, Kreuze J, Fei Z (2017) VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
-|{{#vardefine:app|REPLACE}}
+|{{#vardefine:app|virusdetect}}
-|{{#vardefine:url|REPLACE}}
+|{{#vardefine:url|http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
@@ Line 10: / Line 10: @@
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}