I have been using Galaxy.org for a couple of months now. It is such a powerful platform.
I have two questions regarding the consensus sequence. I was able to MAP with BWA using my NGS data against reference genome. At this point, how can I export the consensus sequence to use for the blast? Or should I use another command to get the consensus sequence from SAM file? Second question is which command should I use to do de novo alignment with NGS data without using the reference genome ?