Virus Detect

Description

This tool runs the VirusDetect pipeline, 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.

More detailed definition of Virus detect pipeline can be found from the home page of VirusDetect.

Input data

Input data (the 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 as reports. Output related options are used to select, what data is returned. By default VirusDtetect returns following files: If parameter Return matching reference sequences is turned on the also following files are returned If parameter Return matching reference sequences is turned on the also 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 Genome Browser to visualize the BLAST reulst. 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.

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