MaskPrimers.py - Removes primers and annotates sequences with primer and barcode identifiers

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

MaskPrimers.py 0.6.0                                May 2020                                   MASKPRIMERS.PY(1)

       usage: MaskPrimers.py [--version] [-h]  ...

       Removes primers and annotates sequences with primer and barcode identifiers

   help:--version
              show program's version number and exit

       -h, --help
              show this help message and exit

   subcommands:
              Alignment method

       align  Find primer matches using pairwise local alignment.

       score  Find primer matches by scoring primers at a fixed position.

       extract
              Remove and annotate a fixed sequence region.

   outputfiles:
              mask-pass

              processed reads with successful primer matches.

              mask-fail

              raw reads failing primer identification.

   outputannotationfields:
              SEQORIENT

              the orientation of the output sequence. Either F (input) or RC (reverse complement of input).

              PRIMER

              name of the best primer match.

              BARCODE

              the sequence preceding the primer match. Only output when the --barcode flag is specified.

       MaskPrimers.py - Removes primers and annotates sequences with primer and barcode identifiers