VirusDetect

Description

This tool runs the VirusDetect pipeline (please find a flowchart below), that performs virus identification using 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. The proposed 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 FASTQ formatted sequence file. If several FASTQ files are provided, a separate VirusDetect analysis will be done for each file.

Parameters

Output

VirusDetect produces large amount of different files and reports. 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 both the blastn_matching_references.fa + .fai and blastn_matches.bam + .bai (or the corresponding BLASTx files), you can use the Chipster Genome Browser to visualize the BLAST results. In the Genome Browser the blastn_matching_references.fa should be assigned to be used as the genome. Each reference virus sequence is then listed in the Chromosome pull down menu.

When parameter Use input names in output file names is selected, the names of the VirusDetect output files will start with the name of the input file analyzed

If the parameter Return results in one archive file is selected, all the output files are stored to a single tar formatted output file. This feature is useful if you run VirusDetect to several input files at the same time. The .tar formatted output file can be expanded with tool Extract .tar.gz file.

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