The complex task of choosing a de novo assembly: Lessons from fungal genomes
Three key parameters of a typical short read sequencing and de novo assembly design are the read length, the insert size and a bioinformatic parameter, the k-mer length (k); k is easy to modify, and one can monitor the effects of its variation before choosing a final k-mer length or assembly. The success and the complexity of a de novo genome assembly task depend on one's needs or priorities: gene space, all the unique DNA, or entire genome with all its repeats. When one restricts a fungal de novo assembly task to a mapping of the gene space by reliable sequences, k often plays only a very minor role, but a correct choice of k can be far from trivial if one needs to map the genome's repetitive regions. Plotting metrics that assess presence of DNA and its genes and repeats in a de novo assembly versus k-mer length used can give valuable insight into an assembly process and its variation.
genome assembly methods repetitive dna next-generation sequencing