MutChromSeq is a method to clone genes in plants. Prerequisites are that the gene must be related to a specific phenotype and that chromosome flow sorting is established in the species. In a nutshell, you do an EMS mutagenesis screen of your wildtype and look for mutants that have lost the phenotype related to your gene. You need at least 5 or 6 independent mutants. If you have been working on that gene for a while, you most problably know on which chromosome it is. Otherwise find out. Flow sort chromosomes of your wildtype and mutants. Sequence amplified DNA from your chromosomes on Illumina. You need about a HiSeq2000 lane per chromosome. A denovo assembly of the wildtype data will be used as reference. You map the mutants against that reference and will find one or very few genes that have a mutation in every of your mutants. Here you find the pipeline and scripts for the analysis of the data.