Extraction of long k-mers using spaced seeds

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 tend to be more accurate when the used are unique analyzed DNA, and thus use longer preferred. When read lengths short technologies increase, error rate will become determining factor for largest possible value k. Here we propose LoMeX which uses spaced seeds extract long accurately even presence errors. Our experiments show that can current Illumina with a higher recall than standard k-mer counting tool. Furthermore, our simulated data length further increases, performance counters declines, whereas still extracts successfully.