im newbie to NGS and linux. can anyone kindly let me know the easiest way to split the fasta file containing chromosome and scaffold into individual files i.e files containing one chromosome per file...
thanks
A modification of Pierre's answer from here : https://www.biostars.org/p/76716/

    awk '/^>/ {F=substr($0, 2, length($0))".fasta"; print >F;next;} {print >> F;}' < ref_genome.fasta

Just replace `ref_genome.fasta` with your file