I am working with population specific re-sequenced genome data from A. lyrata. I need to align it to the reference genome which is already available and prepare population specific sequence. I will also do variant calling but for now alignment of fragment to reference genome is what I am interested in.
Could anyone suggest of a pipeline/apps combination that would be helpful for this purpose?
Thanks RS. I had read about this but I need something that has documentation and potentially already worked out examples to guide me through the process. Examples always help me understand the data better and helps with interpretation. I have been trying to work with BBmap but for right now I am trying to get it work first. I will see how it goes.
Did you look at (read Google) the tools available for short read alignment?
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment