Illumina host / virus read subtraction by short read mapping algorithms (n/n = % of read / % identity).

<p>Illumina host / virus read subtraction by short read mapping algorithms (n/n = % of read / % identity).</p

Idiopathic hepatitis liver datasets: a) Read reduction following mapping subtraction and k-mer similarity filtering.

<p>b) Effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on post-assembly contig number. c) Effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on viral contig size and reference coverage.</p

Optimal word size for viral assembly with multiple assemblers.

<p>Optimal word size for viral assembly with multiple assemblers.</p

Effect of viral reference coverage of Illumina reads (red text), host mapping subtraction (Map), k-mer filtering (k-mer) and low-complexity filtering (LC) on viral contig size and reference coverage (post-assembly) using CLC assembler (v.6) at optimal word size.

<p>Effect of viral reference coverage of Illumina reads (red text), host mapping subtraction (Map), k-mer filtering (k-mer) and low-complexity filtering (LC) on viral contig size and reference coverage (post-assembly) using CLC assembler (v.6) at optimal word size.</p

Human viral simulated dataset: effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on post-assembly contig number.

<p>Human viral simulated dataset: effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on post-assembly contig number.</p

Reports of novel animal virus species in PubMed over the last two decades.

<p>Reports of novel animal virus species in PubMed over the last two decades.</p

a) Simulated dataset: effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on viral contig size and reference coverage.

<p>b) Simulated dataset: Effect of pre-assembly read filters on post-assembly N25-N90 (methods).</p

Host mapping subtraction by reference set.

<p>Host mapping subtraction by reference set.</p

Effect of viral reference coverage of Illumina reads (red text), host mapping subtraction (Map) and k-mer filtering (K-mer) on viral contig size and reference coverage (post-assembly) using different assembly algorithms (Meta = metacortex).

<p>Each assembly algorithm used at optimal k-mer size.</p

SURPI assembled contigs comparison: a) contig coverage of viral references (artificial metagenomics viral dataset) range and mean.

<p>SURPI SD = 28, Mapper SD = 15.5, MAP+k-mer SD = 25.9. b) HCV viral infected liver tissue NGS datasets at 9x and 0.7x coverage with Largest viral assembled contig (blue) and total viral reference coverage of all contigs (red).</p