laxmangene7/Introgression-Mapping-using-Sequencing

Plant Breeder frequently uses alien introgression, i.e. utilizing valuable genes from the wild relatives to the cultivated crop varieties. Traditionally, the introgression of a piece or whole arm of alien chromosomes into the elite varities was confirmed using cytogenetic tools such as FISH and GISH. With the advent of new high-throughput sequencing technology, we can use sequencing of putative introgressed lines to confirm the introgressions. This pipeline uses some other pipelines and basic unix codes to map reads of the introssion lines to a combined reference genome i.e. reference generated through combining the reference genomes of both donor and the recepient.