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.