Effect of k-mer filtering (k-mer) / mapper subtraction (Map) and lowcomplexity filtering (LC) on post-assembly contig numbers.

<p>Effect of k-mer filtering (k-mer) / mapper subtraction (Map) and lowcomplexity filtering (LC) on post-assembly contig numbers.</p

Effect of k-mer filtering (K-mer)/ mapper subtraction (Map) on post-assembly contig number using multiple optimized assemblers with the HCV 9x mean coverage Illumina read dataset.

<p>Effect of k-mer filtering (K-mer)/ mapper subtraction (Map) on post-assembly contig number using multiple optimized assemblers with the HCV 9x mean coverage Illumina read dataset.</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

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

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

Additional file 1 of Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

Additional file 1. Multiplex PCR primer information. List of PCR primer sequences used for multiplex amplification of dengue virus serotypes 1–4. Primer positions indicate the expected binding location based on the RefSeq genome for each serotype, with the appropriate accession number indicated in brackets. Two multiplex PCR reactions should be performed per sample, using either primers indicated as pool 1 or pool 2 in separate reactions