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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