Miscellaneous scripts I find useful:
(1) 'sort_by_chr.sh' #found it frustrating to try to sort large files with multiple chromosomes, so I wrote a shell program that takes a list of chromosomes and an input file and sorts each chromosome on its own, writing it all to output.
(2) 'split_by_chr.pl' #program takes a fasta input and writes an individual output fasta file for each fasta entry. Setup to exclude unknown chromosomes etc (modify for your organism).
For citing purposes: http://dx.doi.org/10.5281/zenodo.10287