  The extraction of k-mers from sequencing reads is an important task in many
bioinformatics applications, such as all DNA sequence analysis methods based on
de Bruijn graphs. These methods tend to be more accurate when the used k-mers
are unique in the analyzed DNA, and thus the use of longer k-mers is preferred.
When the read lengths of short read sequencing technologies increase, the error
rate will become the determining factor for the largest possible value of k.
Here we propose LoMeX which uses spaced seeds to extract long k-mers accurately
even in the presence of sequencing errors. Our experiments show that LoMeX can
extract long k-mers from current Illumina reads with a higher recall than a
standard k-mer counting tool. Furthermore, our experiments on simulated data
show that when the read length further increases, the performance of standard
k-mer counters declines, whereas LoMeX still extracts long k-mers successfully.
