You just downloaded your favorite genome. It’s huge fasta file and now you want to do something with it, but running it on this single file would take forever. You need to split it by chromosomes or contigs, but you are not on your favorite computer where your magic toolbox is installed. Worry no more! As always, UNIX has many built-in tools, that can do anything, but people rarely talk about them.

csplit panTro5.fa /\>chr.*/ {*} 
#every sequence is now in one file named xxx something

for a in x*; do echo $a; mv $a $(head -1 $a).txt; done; 
#we just renamed each file by using first line of each file

Of course, if you fasta header contained anything other than >chr in the header, you would modify you csplit command and replace chr with whatever characters your headers start with. Luckily, you can use csplit to split any files, making it robust and useful tool for bioinformatics that is being flooded by new file formats as we speak..