fasta_clean.py, for cleaning fasta files.
This script will remove all contigs that have coverage below 5 or lengths below 500 bp.
It will also scan the beginning and the end of each contig for garbage sequences, for example, a sequence ending in ...GAGCTAGCTGGCTTGAGCTACGTGAGTCTACTGACTACTTTTACTACTAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAATAAAAA would be trimmed to ...GAGCTAGCTGGCTTGAGCTACGTGAGTCTACTGACTACTTTTACTACT
Usage:
python fasta_clean.py [source_directory] [destination_directory]