I have performed a number of targeted sequence captures across multiple species from known cds regions (as at the time of sequencing no reference genomes were available) de novo assembly was then performed creating a database of contigs for each of my species of interest. This was highly successful and I have been able to analyse lots of data.
However, now a reference genome has become available and i would like to do some further analysis. (re-assembling the short reads would be out of the question as the genetic distance between the species captured renders mapping of short reads to the reference ineffectual). I would like to if at all possible align the assembled contigs for each of the species to the reference genome and then extract regions of interest from both the contigs and the genome but cannot think of an effective method of doing so.
I welcome any suggestions