I am starting doing RNA-seq analyses on Phragmites. To improve the assembly quality, I used both genome-guided assembly via close relative species S.italica and De novo assembly. I checked some paper suggesting to combine these two assemblies but without detailed description. My question is how to combine these two fasta files together (using Linux command 'cat' ? ), and how to remove the redundant after combination? What is the recommendation to do this process? Thanks for your help.