User guide for mutation identification by sequencing

Just published in Genome Biology, collaboration with former grad student Korbinian Schneeberger:

User guide for mapping-by-sequencing in Arabidopsis

Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel and Korbinian Schneeberger

Genome Biology 2013, 14:R61 doi:10.1186/gb-2013-14-6-r61

Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.