.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH MASKPRIMERS.PY "1" "May 2020" "MaskPrimers.py 0.6.0" "User Commands"
.SH NAME
MaskPrimers.py \- Removes primers and annotates sequences with primer and barcode identifiers
.SH DESCRIPTION
usage: MaskPrimers.py [\-\-version] [\-h]  ...
.PP
Removes primers and annotates sequences with primer and barcode identifiers
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Alignment method
.TP
align
Find primer matches using pairwise local alignment.
.TP
score
Find primer matches by scoring primers at a fixed position.
.TP
extract
Remove and annotate a fixed sequence region.
.SS "output files:"
.IP
mask\-pass
.IP
processed reads with successful primer matches.
.IP
mask\-fail
.IP
raw reads failing primer identification.
.SS "output annotation fields:"
.IP
SEQORIENT
.IP
the orientation of the output sequence. Either F (input) or RC
(reverse complement of input).
.IP
PRIMER
.IP
name of the best primer match.
.IP
BARCODE
.IP
the sequence preceding the primer match. Only output when the
\fB\-\-barcode\fR flag is specified.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.