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.
Version on CSC's Servers
Version 1.7 is available in Taito and in Chipster
To use VirusDetect in Taito you first need to run set up command for biokit.
module load biokit
After that you can start Virus Detect with command
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 Taito the Silva database is available in path:
The actual clening command could look like:
bowtie -v 1 -k 1 --un cleaned_reads.fastq -f -q -p 4 /proj/csc/biosci/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 Taito environment. This means that users have to do the BWA indexing for their host organism genome before running VirusDetect.
For example for Arabidopsis thaliana the required BWA indexes can be created with commands:
ensemblfetch arabidopsis_thaliana mv Arabidopsis_thaliana.TAIR10.dna.toplevel.fa a_thaliana.fa bwa index -p a_thaliana a_thaliana.fa
After which you can launch the virus detect job with command:
virus_detect.pl --reference vrl_plant --host_reference a_thaliana.fa cleaned_reads.fastq
Both the Virus Detect and BWA indexing task require often significant computing capacity. Because of that, you should use either batch jobs or taito-shell.csc.fi environment for running Virus Detect jobs. Below is a sample batch job file for running Virus Detect with 4 computing cores and 8 GB of memory. The maximum running time in the job below is set to 10 hours.
#!/bin/bash -l #SBATCH -J Virus_detect #SBATCH -o output_%j.txt #SBATCH -e errors_%j.txt #SBATCH -t 10:00:00 #SBATCH -n 1 #SBATCH --nodes=1 #SBATCH --cpus-per-task=4 #SBATCH -p serial #SBATCH --mem=8000 # module load biokit virus_detect.pl --thread_num 4 --reference vrl_plant --host_reference a_thaliana.fa reads.fastq
The batch job file above can be submitted to the batch job system with command:
sbatch batch_job_file.shMore information about running batch jobs in Taito can be found from Chapter 3 of the Taito user guide.