MASKPRIMERS.PY

NAME

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

DESCRIPTION

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.

output files:

mask-pass

processed reads with successful primer matches.

mask-fail

raw reads failing primer identification.

output annotation fields:

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.

AUTHOR

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