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Is it possible to use HiFi reads to call base modifications?

Base modifications can be inferred from per-base pulse width (PW) and inter-pulse duration (IPD) kinetics. Running ccs with --hifi-kinetics generates averaged kinetic information for polished reads, independently for both strands of the insert. Forward is defined with respect to the orientation represented in SEQ and is considered to be the native orientation. As with other PacBio-specific tags, aligners will not re-orient these fields.

Minor cases exist where a certain orientation may get filtered out entirely from a ZMW, preventing valid values from being passed for that record. In these cases, empty lists will be passed for the respective record/orientation and number of passes will be set to zero.

In order to facilitate the use of HiFi reads with base modifications workflows, we have added an executable in pbbam called ccs-kinetics-bystrandify which creates a pseudo --by-strand BAM with corresponding pw and ip tags that imitates a normal, unaligned subreads BAM. You can install pbbam from Bioconda by calling conda install pbbam.