Linkage maps and genotype data of strawberry produced with skim-sequencing data

The following set of files contain the results and scripts to produce those results, described in Chapter 5 of the PhD thesis of Alejandro Thérèse Navarro, entitled "How to map a million markers: linkage mapping of skim-sequencing data in strawberry". In this study, a large dataset of markers produced by whole genome resequecning of a strawberry (<em>Fragaria </em>x <em>ananassa</em>) biparental population are used to generate linkage maps. To that end the software Smooth Descent is used, since it is oriented to obtaining linkage maps in usin low quality (error-prone) genotype data. With this methodology we were able to produce a linkage map of 27 out of 28 chromosomes of strawberry which containing 1.85M markers in ~2400 unique genetic mpositions. We also compare this map with a linkage map produced using SNP array data and with the genome sequence assembly "Camarosa".