This tool runs the VirusDetect pipeline (please find a flowchart below), that performs virus identification using small RNA (sRNA) sequencing data. Given a FASTQ file, it performs de novo assembly and reference-guided assembly by aligning sRNA reads to the reference database of known viruses. The assembled contigs are compared to the reference virus sequences for virus identification first using BLASTN and then BLASTX. Virus assignments are selected based on the three cutoff parameters described below.

More detailed description of the VirusDetect pipeline is available at the home page of VirusDetect.

Input data

Input data (reads) should be given as a FASTQ formatted sequence file. If several FASTQ files are provided, a separate VirusDetect analysis will be done for each file.



VirusDetect produces a large number of result files. Output related options are used to select, what data is returned. By default VirusDetect returns the following files: If the parameter Return matching reference sequences is turned on, also the following files are returned If the parameter Return BAM formatted alignments is turned on, also the following files are returned

Note: If you select the blastn_matching_references.fa and blastn_matches.bam, you can use the Chipster Genome Browser to visualize the BLAST results. In the Genome Browser the blastn_matching_references.fa is used as the genome and each reference virus sequence is listed in the Chromosome pull down menu.

Figure 1.Flowchart of the VirusDetect pipeline. Green boxes indicate the output files. Steps where the parameters are used are indicated with blue letters.