Advanced parameters

We currently expose four parameters that allow you to tweak the behavior of the algorithm.

As briefly mentioned above, you can use the -f/--fraction parameter (default value is 30) to control how the distinction between long reads and short reads is made. By default, the longest reads corresponding to 30% of the total read length are considered "long".

Once all the short reads have been mapped to the long reads, you have the option of adjusting three filtering criteria. If short-on-long coverage falls beneath the value provided after the -m/--min-coverage parameter, those parts of the corrected long read are excised, resulting in several, shorter reads. Those shorter reads are then filtered according to the following two parameters:

Here is a complete example, where we correct the PacBio reads contained in raw_reads.fa and, producing a single file containing the corrected long reads corrected_reads.fa:

clc_correct_pacbio_reads -q raw_reads.fa -o corrected_reads.fa
                         -f 30 -m 10 -l 1000 -a 15