I'm currently working on whole exome data and I wanted to know if it's better to map the reads against a reference genome directly. Or is it better to first make a de novo assembly which will give me hopefully a number of contig corresponding to the number of sequenced exon (~200,000) and then map those contigs against the reference genome?
What do you think? Could it possibly improve the final mapping?
If yes which de novo assembly tool would you recommend me?