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.