Difference between revisions of "DVGfinder"

Latest revision as of 13:59, 31 July 2023

Description

DVGfinder is a tool that integrates the most used DVGs search algorithms, ViReMa-a and DI-tector, in a unique workflow, making the analysis of a sample easier and more intuitive. Also, DVGfinder_v3 implements a Gradient Boosting classifier to try to reduce the number of false positives introduced by the search algorithms and generates an HTML report with interactive tables and plots that facilitates a first exploration of the results.

Environment Modules

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

System Variables

HPC_DVGFINDER_DIR - installation directory
HPC_DVGFINDER_BIN - executable directory

Additional Information

To run DVGfinder:

$ git clone https://github.com/MJmaolu/DVGfinder.git
$ cd DVGfinder
$ chmod -R +x .
$ module load dvgfinder

Follow the DVGfinder README 'Usage' instructions

@@ Line 2: / Line 2: @@
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|dvgfinder}}
-|{{#vardefine:url|https://mjmaolu.github.io/DVGfinder/}}
+|{{#vardefine:url|https://github.com/MJmaolu/DVGfinder}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 26: / Line 26: @@
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_{{uc:{{#var:app}}}}_BIN - executable directory
-* HPC_{{uc:{{#var:app}}}}_REF - reference data directory
 <!--Configuration-->
@@ Line 34: / Line 33: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-DVGfinder should be run with:
+To run DVGfinder:
-  dvgfinder -fq path_to_fastq_file [-r path_to_fasta_virus_reference] [-m margin] [-t threshold] [-n number_processes] [-s polarity]
+  $ git clone https://github.com/MJmaolu/DVGfinder.git
+ $ cd DVGfinder
+ $ chmod -R +x .
+ $ module load dvgfinder
+Follow the DVGfinder README 'Usage' instructions
 |}}