Results of <i>Solanum</i> Sanger sequencing.

<p>We chose 27 predicted SNPs to test with Sanger sequencing. These were chosen from the Bubbleparse ranked list according to four sets of criteria, with all SNPs placed within the top 22,000 of the 68,000 linked SNPs at the expected heterozygosity. The largest number, 10, were chosen from the top of the list, which contains bubbles which are close to the expected allele ratio and also of high coverage. A second group were chosen which were very close to the expected allele ratio, but not such good coverage. A third group had very good coverage, but were not so close to the expect allele ratio. Finally, a fourth group was chosen which had high quality scores, but not necessarily as close a ratio or as good a coverage as previous groups. Overall, we found a high rate of true SNPs – with 23 out of 27 sequences containing a SNP in the position predicted by Bubbleparse, of which 14 displayed the predicted heterozygous alleles. The group chosen from the top of the ranked list showed high accuracy, with 9 out of 10 SNPs confirmed, but high rates were also shown for the other groups, though sample sizes were small.</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

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

Types of <i>Solanum</i> SNPs discovered by Bubbleparse.

<p>Graph showing the types of SNPs discovered by Bubbleparse for the cross between <i>Phytophthora infestans</i> resistant <i>Solanum berthaultii</i> and susceptible <i>Solanum stenotomum</i>. Because of the nature of the cross, we expect to find heterozygous resistance-linked SNPs and Bubbleparse produced a list of 68,084 of these, from which we selected 27 for sequencing.</p

Results of <i>Arabidopsis thaliana</i> Sanger sequencing.

<p>From the ranked list of all SNPs predicted by Bubbleparse in contigs of over 200 nt, the top 48, as well as 16 from 25%, 50% and 75% down the list were tested with Sanger sequencing. This confirmed all but 5 as being real SNPs between Col-0 and Ler-1. The remaining five all had sequencing problems – such as the sequence ending before the SNP was reached – so are not confirmed as false postives.</p

Optimal word size for viral assembly with multiple assemblers.

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

Effect of depth of search on number of bubbles found by Bubbleparse.

<p>Graphs showing numbers of bubbles found for Bur-0 and Tsu-1 with search depth set to 0, 1, 2 and 3 at constant read coverage (top) and for Ler-1 at varied read coverage (bottom).</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