<p>How does the kmer length affect the total assembly size and the N50 statistic with single end-reads and why?</p>

<p>Very generally spoken:</p>

<p>With larger kmer size there is a better chance of avoiding ambiguities in the graph between similar regions (repeats, paralogs,...). Ambiguities occur if kmer exist multiple times within the genome. (Unresolvable) ambiguities terminate contigs, hence larger kmer sizes in theory increase N50. However, large kmer sizes are much more sensitive to sequencing errors, heterozygosity and coverage.<br />
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Assembly size depends on how the assembler handles small ambiguities (bubbles) in the graph and how it handles low coverage paths. With small kmer sizes and some sensitivity to bubbles, you are more likely to generate a single contig for a slightly noisy region. This might be good in case of SNPs or bad if you merge repeats, .... This effect leads to smaller assembly size for small kmers. With large kmers you are more likely to generate different fragments for exiting variants, which increases assembly size. However, if these fragments fail for example internal coverage or length cutoffs, the final assembly may actually be smaller.</p>
