Can I produce one consensus sequence for each strand of a molecule?
Yes, please use --by-strand
. Make sure that you have sufficient coverage, as --min-passes
are per strand in this case. For each strand, ccs generates one consensus read that has to pass all filters. Read name suffix indicates strand. Example:
m64011_190714_120746/14/ccs/rev
m64011_190714_120746/35/ccs/fwd
How does --by-strand
work? For each ZMW:
- Determine orientation of reads with respect to the one closest to the median length
- Sort reads into two buckets, forward and reverse strands
- Treat each strand as an individual entity as we do with ZMWs
- Apply all filters per strand individually
- Create a draft for each strand
- Polish each strand
- Write out each polished strand consensus