Paired reads

Paired reads often come split across two files: one containing the first mates, paired_1.fa:

Image mapper_read_file_1

and one containing the second mates, paired_2.fa:

Image mapper_read_file_2

Use the -p/--paired parameter to indicate that the following files contain paired reads of a certain type, and use the -i/--interleave parameter to pair up the two files: 

clc_mapper -q -p fb ss 50 500 -i paired_1.fa paired_2.fa ...
Behind the scenes, the pairs are interleaved and processed together:

Image mapper_read_file_both

If you have a paired file, that is already interleaved, you can leave out the -i/--interleave parameter: 

clc_mapper -q -p fb ss 50 500 interleaved_pairs.fastq ...
For detailed information about the -p fb ss 50 500 parameter, please refer to Paired read considerations.