Single reads
In the case of single reads, you simply list the files after the-q/--reads parameter:
clc_mapper -q single_reads.fastq more_single_reads.fasta ...In the special case of PacBio reads, you can optimize both quality and speed of the alignment process by providing type information as follows:
clc_mapper -q --type pacbio long_pacbio_reads.fastq ...The type, as defined by the
--type parameter, applies to all following files.