Example of duplicate read removal

The following command outputs all reads to coli_reads_nodup.fa that are not identified as duplicates from the paired reads contained in coli_reads_1/2.fa and coli_reads_2/2.fa. 

clc_remove_duplicates -p -r -i coli_reads_1/2.fa coli_reads_2/2.fa
                    -o coli_reads_nodup.fa

The program runs only in a single thread and for large data set it would be convenient to run multiple instances at the same time for each data file.