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VirusDetect

Description

VirusDetect is a software for analyzing 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.

License

Developers state that the software is free to use and open source, do not provide a specific license.

Available

  • Puhti: 1.7
  • Chipster graphical user interface

Usage

To use VirusDetect in Puhti you first need to load biokit and virusdetect modules. 

module load biokit
module load virusdetect
After that you can start Virus Detect with command virus_detect.pl. For example: 
virus_detect.pl --reference vrl_plant reads.fastq
The developers of VirusDetect recommend to remove ribosomal RNA (rRNA) sequences from the input sequences before running VirusDetect. This can be done by aligning the sRNA reads against Silva rRNA database using Bowtie. In Puhti the Silva database is available in path:

/appl/data/bio/biodb/production/silva/Silva_rRNA_database

The actual cleaning command could look like: 

bowtie -v 1 -k 1 --un cleaned_reads.fastq  -f -q /appl/data/bio/biodb/production/silva/Silva_rRNA_database reads.fastq  sRNA_rRNA_match

If possible, it is recommended that you use --host_reference option to filter out the sRNA originating from the host organism. This filtering is done by running a BWA mapping against the genome of the host organism. CSC is not maintaining BWA indexes in Puhti environment, but you can use chipster_genomes to retrieve bwa indexes used by the Chipster service.

chipster_genomes bwa
The command above lists the available indexes and asks you to pick one. If a suitable species is not available, then you need to do indexing for their host organism genome before running VirusDetect.

For example for Triticum aestivum the required BWA indexes can be created with commands: 

ensemblfetch.sh triticum_aestivum
mv Triticum_aestivum.IWGSC.dna.toplevel.fa triticum_aestivum.fa
bwa index -p triticum_aestivum triticum_aestivum.fa
Note that generating BWA indexes for plant genomes can take several hours.

Once you have the BWA index fo the host genome available, you can launch the VirusDetect job with command:

virus_detect.pl --reference vrl_plant --host_reference  triticum_aestivum.fa cleaned_reads.fastq

VirusDetect is mainly used for detecting plant viruses (vrl_plant), but you can use it for other viruses too. The --reference option defines the reference virus sequence dataset to be used. The available reference datasets are: 

vrl_algae
vrl_bacteria
vrl_fungus
vrl_invertebrates
vrl_plants
vrl_vertebrates

Both the Virus Detect and BWA indexing task require often significant computing capacity. Because of that, you should use batch jobs for running Virus Detect jobs. Below is a sample batch job file for running Virus Detect with 8 computing cores and 8 GB of memory. The maximum running time in the job below is set to 10 hours.

#!/bin/bash -l
#SBATCH --job-name=VirusDetect
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --account=your_project_name
#SBATCH --time=10:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --partition=small
#SBATCH --mem=8000
#

module load biokit
module load virusdetect

virus_detect.pl --thread_num 8 --reference vrl_plants --host_reference triticum_aestivum.fa reads_123.fastq

The batch job file above can be submitted to the batch job system with command: 

sbatch batch_job_file.sh
More information about running batch jobs in Puhti can be found from batch job instruction pages.

VirusDetect wites the analysys results to a new directory, named after the query dataset: result_queryfile. VirusDetect produces a large number of result files. The most essential files are:

  • blastn.html Table listing reference viruses that have corresponding virus contigs identified by BLASTN.
  • blastx.html Table listing reference viruses that have corresponding virus contigs identified by BLASTX.
  • query.blastn.xls Table of BLASTN matches to the reference virus database.
  • query.blastx.xls Table of BLASTX matches to the reference virus database.
  • undetermined.html Table listing the length, siRNA size distribution and 21-22nt percentage of undetermined contigs. Potential virus contigs (21-22 nt > 50%) are indicated in green.
  • undetermined_blast.html Table listing contigs having hits in the virus reference database but not assigned to any reference viruses because they did not meet the coverage or depth criteria.

As many of the output files are in html format, it may be difficult to study them in Puhti. One option to study the results is to move them to a public bucket in Allas. For example (replace projnum with your own project number): 

module load allas
allas-conf
rclone copy -P results_cleaned_reads.fastq allas:virusdetect_projnum/results_cleaned_reads.fastq/
a-publish -b virusdetect_projnum -index dynamic
Now you can study the results with your local browser in URL: 
https://a3s.fi//virusdetect_projnum/index.html

More information