Identify Viral Integration Sites

This tool searches for likely viral/host integration events. The tool works by searching for regions with reads with unaligned ends and/or discordant paired reads, where one read in the pair maps to the host, and the other read maps to a virus.

Notice: this tool can only be used for protocols such as hybrid capture, which specifically enriches for viral genomes while capturing at least some chimeric reads that map to both host and virus genomes.

The approach is the following:

To start the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Taxonomic Analysis (Image taxonomic_analysis_folder_closed_16_n_p) | Identify Viral Integration Sites (Image identify_viral_integration_sites_16_n_p)

The Identify Viral Integration Sites tool takes one or several single or paired-end read files as input.

After selecting the input reads, it is possible to specify the host and virus references, and adjust the detection parameters, see (figure 6.15).

The following parameters are available:

Image viral_integration_step1
Figure 6.15: Select references and adjust detection options.

The final step is to specify the output objects, see (figure 6.16). The following options are available:

Image viral_integration_step2
Figure 6.16: Select output options.