Fig. 5

The diagram illustrates the analysis pipelines for the virus detection process. a High concentration viruses allow de novo assembly to construct the genome. The contigs are tested with BLAST and the nt-database for known viruses and the selected virus genomes coverage plotted. (b) The k-mer content of the reads is inspected with Kraken and if the presence of a virus is supported by a high number of reads, the references are downloaded and reads aligned to them. (c) If a reference genome is available, the reads can be directly aligned. For flows (b) and (c) the read depth against genome position can be plotted