The purpose of the last three sections in this chapter on de novo assembly is to introduce two new tools that we have made specifically to assist with long read assembly. Note that both tools are still considered beta quality, and that they have exclusively been tested with PacBio data.
The two tools work in tandem:
clc_correct_pacbio_readstool (optionally) error-corrects PacBio reads, leading to a much improved subsequent PacBio assembly.
clc_assembler_longis our long read de novo assembler.
In the next two subsections, we will show you how to use the two tools.