some scripts to process fasta and fastq sequences

This script takes a fasta file from STDIN, removes duplicated sequences and writes the output to STDOUT.

Sequences will be deleted, if they have an identical header and an identical sequence. This script can also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters are converted to N. This feature can be skipped using the –no-convert option. The script also converts lowercase sequence characters to uppercase. This can be skipped with the –no-up option.

Use one the following commands for help:

./remove_dulicates --help
perldoc ./remove_duplicates